===================================================================================== _____ _______ __ __ _______ ______ ___ ______ _______ / ___\ ____ / ____// \ / / / ____/| _ \ \ \ | _ \ / ____/ / /____| _ \| |___ | \| || |___ | |_] || | | |_] | |___ | /|__ | |_) | ___| | || ___| | ___/ | | | ___/| ___| \ \__| | _ <| |____ | |\ || |____ | | | | | | | |____ \______/|_| \_\_______\/__| \__|\_______\|__| \___\|__| \_______\ Date: 2024-07-29 13:38:34 Platform: Linux-4.12.14-197.108-default-x86_64-with-SuSE-15-x86_64 #1 SMP Tue Mar 1 18:11:35 UTC 2022 (2b1bf36) Host: cm2login1 User: ra35naf Conda: 22.9.0 Python: 3.7.10 Snakemake: 6.0.5 Grenepipe: 0.12.2 Conda env: grenepipe (/dss/dsshome1/lxc0C/ra35naf/miniconda3/envs/grenepipe) Command: /dss/dsshome1/lxc0C/ra35naf/miniconda3/envs/grenepipe/bin/snakemake --profile profiles/slurm --directory /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2022__Pmon_pop_gen/1__preprocessing/5__repeat_vc/output_new --conda-frontend mamba --conda-prefix /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2022__Pmon_pop_gen/1__preprocessing/5__repeat_vc/grenepipe-0.12.2/envs --jobs 50 --reason -n Base directory: /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2022__Pmon_pop_gen/1__preprocessing/5__repeat_vc/grenepipe-0.12.2 Working directory: /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2022__Pmon_pop_gen/1__preprocessing/5__repeat_vc/output_new Config file(s): /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2022__Pmon_pop_gen/1__preprocessing/5__repeat_vc/output_new/config.yaml Samples: 93, with 146 total units ===================================================================================== Building DAG of jobs... Updating job merge_variants. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Updating job map_reads. Job counts: count jobs 1 all 39 bam_index 1 bcftools_stats 1 bcftools_stats_plot 1057 call_variants 27 combine_calls 2 gatk_hard_filter_calls 27 genotype_variants 1 merge_calls 1 merge_variants 1 multiqc 2 select_calls 1160 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_102.bam output: dedup/N_102.bam.bai log: logs/samtools/index/dedup/N_102.log jobid: 1325 reason: Updated input files: dedup/N_102.bam wildcards: prefix=dedup/N_102 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_689.bam output: dedup/N_689.bam.bai log: logs/samtools/index/dedup/N_689.log jobid: 1421 reason: Updated input files: dedup/N_689.bam wildcards: prefix=dedup/N_689 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_83.bam output: dedup/N_83.bam.bai log: logs/samtools/index/dedup/N_83.log jobid: 1443 reason: Updated input files: dedup/N_83.bam wildcards: prefix=dedup/N_83 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_6489.bam output: dedup/N_6489.bam.bai log: logs/samtools/index/dedup/N_6489.log jobid: 1415 reason: Updated input files: dedup/N_6489.bam wildcards: prefix=dedup/N_6489 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T1483.bam output: dedup/T1483.bam.bai log: logs/samtools/index/dedup/T1483.log jobid: 1463 reason: Updated input files: dedup/T1483.bam wildcards: prefix=dedup/T1483 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T190.bam output: dedup/T190.bam.bai log: logs/samtools/index/dedup/T190.log jobid: 1483 reason: Updated input files: dedup/T190.bam wildcards: prefix=dedup/T190 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_690.bam output: dedup/N_690.bam.bai log: logs/samtools/index/dedup/N_690.log jobid: 1423 reason: Updated input files: dedup/N_690.bam wildcards: prefix=dedup/N_690 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T180.bam output: dedup/T180.bam.bai log: logs/samtools/index/dedup/T180.log jobid: 1469 reason: Updated input files: dedup/T180.bam wildcards: prefix=dedup/T180 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T72.bam output: dedup/T72.bam.bai log: logs/samtools/index/dedup/T72.log jobid: 1497 reason: Updated input files: dedup/T72.bam wildcards: prefix=dedup/T72 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_8583.bam output: dedup/N_8583.bam.bai log: logs/samtools/index/dedup/N_8583.log jobid: 1449 reason: Updated input files: dedup/N_8583.bam wildcards: prefix=dedup/N_8583 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1156.bam output: dedup/N_1156.bam.bai log: logs/samtools/index/dedup/N_1156.log jobid: 1329 reason: Updated input files: dedup/N_1156.bam wildcards: prefix=dedup/N_1156 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T185.bam output: dedup/T185.bam.bai log: logs/samtools/index/dedup/T185.log jobid: 1473 reason: Updated input files: dedup/T185.bam wildcards: prefix=dedup/T185 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_6490.bam output: dedup/N_6490.bam.bai log: logs/samtools/index/dedup/N_6490.log jobid: 1417 reason: Updated input files: dedup/N_6490.bam wildcards: prefix=dedup/N_6490 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_9104.bam output: dedup/N_9104.bam.bai log: logs/samtools/index/dedup/N_9104.log jobid: 1455 reason: Updated input files: dedup/N_9104.bam wildcards: prefix=dedup/N_9104 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_7.bam, dedup/N_7.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_7.contig-group-0.g.vcf.gz, called/N_7.contig-group-0.g.vcf.gz.tbi, called/N_7.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_7.contig-group-0.log jobid: 1436 benchmark: benchmarks/gatk/haplotypecaller/N_7.contig-group-0.bench.log reason: Missing output files: called/N_7.contig-group-0.g.vcf.gz.tbi, called/N_7.contig-group-0.g.vcf.gz; Updated input files: dedup/N_7.bam, contig-groups/contig-group-0.bed, dedup/N_7.bam.bai wildcards: sample=N_7, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_79.bam output: dedup/N_79.bam.bai log: logs/samtools/index/dedup/N_79.log jobid: 1435 reason: Updated input files: dedup/N_79.bam wildcards: prefix=dedup/N_79 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T193.bam, dedup/T193.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T193.contig-group-5.g.vcf.gz, called/T193.contig-group-5.g.vcf.gz.tbi, called/T193.contig-group-5.g.done log: logs/gatk/haplotypecaller/T193.contig-group-5.log jobid: 1973 benchmark: benchmarks/gatk/haplotypecaller/T193.contig-group-5.bench.log reason: Missing output files: called/T193.contig-group-5.g.vcf.gz, called/T193.contig-group-5.g.vcf.gz.tbi; Updated input files: dedup/T193.bam.bai, contig-groups/contig-group-5.bed, dedup/T193.bam wildcards: sample=T193, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T79.bam output: dedup/T79.bam.bai log: logs/samtools/index/dedup/T79.log jobid: 1499 reason: Updated input files: dedup/T79.bam wildcards: prefix=dedup/T79 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_9449.bam output: dedup/N_9449.bam.bai log: logs/samtools/index/dedup/N_9449.log jobid: 1457 reason: Updated input files: dedup/N_9449.bam wildcards: prefix=dedup/N_9449 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_351.bam output: dedup/N_351.bam.bai log: logs/samtools/index/dedup/N_351.log jobid: 1393 reason: Updated input files: dedup/N_351.bam wildcards: prefix=dedup/N_351 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_6928.bam output: dedup/N_6928.bam.bai log: logs/samtools/index/dedup/N_6928.log jobid: 1427 reason: Updated input files: dedup/N_6928.bam wildcards: prefix=dedup/N_6928 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T196.bam output: dedup/T196.bam.bai log: logs/samtools/index/dedup/T196.log jobid: 1491 reason: Updated input files: dedup/T196.bam wildcards: prefix=dedup/T196 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2002_0292.bam, dedup/N_2002_0292.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_2002_0292.contig-group-2.g.vcf.gz, called/N_2002_0292.contig-group-2.g.vcf.gz.tbi, called/N_2002_0292.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_2002_0292.contig-group-2.log jobid: 1633 benchmark: benchmarks/gatk/haplotypecaller/N_2002_0292.contig-group-2.bench.log reason: Missing output files: called/N_2002_0292.contig-group-2.g.vcf.gz, called/N_2002_0292.contig-group-2.g.vcf.gz.tbi; Updated input files: dedup/N_2002_0292.bam.bai, dedup/N_2002_0292.bam, contig-groups/contig-group-2.bed wildcards: sample=N_2002_0292, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N2005.bam output: dedup/N2005.bam.bai log: logs/samtools/index/dedup/N2005.log jobid: 1323 reason: Updated input files: dedup/N2005.bam wildcards: prefix=dedup/N2005 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_5129.bam output: dedup/N_5129.bam.bai log: logs/samtools/index/dedup/N_5129.log jobid: 1413 reason: Updated input files: dedup/N_5129.bam wildcards: prefix=dedup/N_5129 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1354.bam output: dedup/N_1354.bam.bai log: logs/samtools/index/dedup/N_1354.log jobid: 1339 reason: Updated input files: dedup/N_1354.bam wildcards: prefix=dedup/N_1354 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1609.bam output: dedup/N_1609.bam.bai log: logs/samtools/index/dedup/N_1609.log jobid: 1357 reason: Updated input files: dedup/N_1609.bam wildcards: prefix=dedup/N_1609 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_4847.bam output: dedup/N_4847.bam.bai log: logs/samtools/index/dedup/N_4847.log jobid: 1407 reason: Updated input files: dedup/N_4847.bam wildcards: prefix=dedup/N_4847 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1934_1_1_5973.bam output: dedup/N_1934_1_1_5973.bam.bai log: logs/samtools/index/dedup/N_1934_1_1_5973.log jobid: 1371 reason: Updated input files: dedup/N_1934_1_1_5973.bam wildcards: prefix=dedup/N_1934_1_1_5973 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1870.bam output: dedup/N_1870.bam.bai log: logs/samtools/index/dedup/N_1870.log jobid: 1359 reason: Updated input files: dedup/N_1870.bam wildcards: prefix=dedup/N_1870 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_2003_5409.bam output: dedup/N_2003_5409.bam.bai log: logs/samtools/index/dedup/N_2003_5409.log jobid: 1385 reason: Updated input files: dedup/N_2003_5409.bam wildcards: prefix=dedup/N_2003_5409 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1927.bam output: dedup/N_1927.bam.bai log: logs/samtools/index/dedup/N_1927.log jobid: 1365 reason: Updated input files: dedup/N_1927.bam wildcards: prefix=dedup/N_1927 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_8565.bam output: dedup/N_8565.bam.bai log: logs/samtools/index/dedup/N_8565.log jobid: 1447 reason: Updated input files: dedup/N_8565.bam wildcards: prefix=dedup/N_8565 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T194.bam, dedup/T194.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T194.contig-group-5.g.vcf.gz, called/T194.contig-group-5.g.vcf.gz.tbi, called/T194.contig-group-5.g.done log: logs/gatk/haplotypecaller/T194.contig-group-5.log jobid: 1974 benchmark: benchmarks/gatk/haplotypecaller/T194.contig-group-5.bench.log reason: Missing output files: called/T194.contig-group-5.g.vcf.gz, called/T194.contig-group-5.g.vcf.gz.tbi; Updated input files: dedup/T194.bam.bai, contig-groups/contig-group-5.bed, dedup/T194.bam wildcards: sample=T194, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T192.bam output: dedup/T192.bam.bai log: logs/samtools/index/dedup/T192.log jobid: 1485 reason: Updated input files: dedup/T192.bam wildcards: prefix=dedup/T192 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1158.bam output: dedup/N_1158.bam.bai log: logs/samtools/index/dedup/N_1158.log jobid: 1333 reason: Updated input files: dedup/N_1158.bam wildcards: prefix=dedup/N_1158 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/T187.bam output: dedup/T187.bam.bai log: logs/samtools/index/dedup/T187.log jobid: 1477 reason: Updated input files: dedup/T187.bam wildcards: prefix=dedup/T187 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_4843.bam output: dedup/N_4843.bam.bai log: logs/samtools/index/dedup/N_4843.log jobid: 1401 reason: Updated input files: dedup/N_4843.bam wildcards: prefix=dedup/N_4843 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1386.bam output: dedup/N_1386.bam.bai log: logs/samtools/index/dedup/N_1386.log jobid: 1345 reason: Updated input files: dedup/N_1386.bam wildcards: prefix=dedup/N_1386 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1157.bam output: dedup/N_1157.bam.bai log: logs/samtools/index/dedup/N_1157.log jobid: 1331 reason: Updated input files: dedup/N_1157.bam wildcards: prefix=dedup/N_1157 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_8171.bam output: dedup/N_8171.bam.bai log: logs/samtools/index/dedup/N_8171.log jobid: 1441 reason: Updated input files: dedup/N_8171.bam wildcards: prefix=dedup/N_8171 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/N_1992_0123.bam output: dedup/N_1992_0123.bam.bai log: logs/samtools/index/dedup/N_1992_0123.log jobid: 1375 reason: Updated input files: dedup/N_1992_0123.bam wildcards: prefix=dedup/N_1992_0123 [Mon Jul 29 13:38:42 2024] group job mapping_extra (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule bam_index: input: dedup/M5672.bam output: dedup/M5672.bam.bai log: logs/samtools/index/dedup/M5672.log jobid: 1319 reason: Updated input files: dedup/M5672.bam wildcards: prefix=dedup/M5672 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/M5672.contig-group-25.g.vcf.gz, called/M5672.contig-group-25.g.vcf.gz.tbi, called/M5672.contig-group-25.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-25.log jobid: 3809 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-25.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T196.contig-group-0.g.vcf.gz, called/T196.contig-group-0.g.vcf.gz.tbi, called/T196.contig-group-0.g.done log: logs/gatk/haplotypecaller/T196.contig-group-0.log jobid: 1490 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-0.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T192.contig-group-23.g.vcf.gz, called/T192.contig-group-23.g.vcf.gz.tbi, called/T192.contig-group-23.g.done log: logs/gatk/haplotypecaller/T192.contig-group-23.log jobid: 3700 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-23.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T190.contig-group-12.g.vcf.gz, called/T190.contig-group-12.g.vcf.gz.tbi, called/T190.contig-group-12.g.done log: logs/gatk/haplotypecaller/T190.contig-group-12.log jobid: 2643 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-12.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_9449.contig-group-21.g.vcf.gz, called/N_9449.contig-group-21.g.vcf.gz.tbi, called/N_9449.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-21.log jobid: 3494 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_351.contig-group-1.g.vcf.gz, called/N_351.contig-group-1.g.vcf.gz.tbi, called/N_351.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-1.log jobid: 1542 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T192.contig-group-5.g.vcf.gz, called/T192.contig-group-5.g.vcf.gz.tbi, called/T192.contig-group-5.g.done log: logs/gatk/haplotypecaller/T192.contig-group-5.log jobid: 1972 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-5.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T79.contig-group-24.g.vcf.gz, called/T79.contig-group-24.g.vcf.gz.tbi, called/T79.contig-group-24.g.done log: logs/gatk/haplotypecaller/T79.contig-group-24.log jobid: 3803 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-24.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1157.contig-group-3.g.vcf.gz, called/N_1157.contig-group-3.g.vcf.gz.tbi, called/N_1157.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-3.log jobid: 1703 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T185.contig-group-21.g.vcf.gz, called/T185.contig-group-21.g.vcf.gz.tbi, called/T185.contig-group-21.g.done log: logs/gatk/haplotypecaller/T185.contig-group-21.log jobid: 3502 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-21.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T190.contig-group-26.g.vcf.gz, called/T190.contig-group-26.g.vcf.gz.tbi, called/T190.contig-group-26.g.done log: logs/gatk/haplotypecaller/T190.contig-group-26.log jobid: 3987 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-26.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T185.contig-group-12.g.vcf.gz, called/T185.contig-group-12.g.vcf.gz.tbi, called/T185.contig-group-12.g.done log: logs/gatk/haplotypecaller/T185.contig-group-12.log jobid: 2638 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-12.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T185.contig-group-24.g.vcf.gz, called/T185.contig-group-24.g.vcf.gz.tbi, called/T185.contig-group-24.g.done log: logs/gatk/haplotypecaller/T185.contig-group-24.log jobid: 3790 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-24.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_8171.contig-group-18.g.vcf.gz, called/N_8171.contig-group-18.g.vcf.gz.tbi, called/N_8171.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-18.log jobid: 3198 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1158.contig-group-16.g.vcf.gz, called/N_1158.contig-group-16.g.vcf.gz.tbi, called/N_1158.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-16.log jobid: 2952 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T187.contig-group-24.g.vcf.gz, called/T187.contig-group-24.g.vcf.gz.tbi, called/T187.contig-group-24.g.done log: logs/gatk/haplotypecaller/T187.contig-group-24.log jobid: 3792 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-24.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T180.contig-group-26.g.vcf.gz, called/T180.contig-group-26.g.vcf.gz.tbi, called/T180.contig-group-26.g.done log: logs/gatk/haplotypecaller/T180.contig-group-26.log jobid: 3980 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-26.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_9449.contig-group-19.g.vcf.gz, called/N_9449.contig-group-19.g.vcf.gz.tbi, called/N_9449.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-19.log jobid: 3302 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_5129.contig-group-0.g.vcf.gz, called/N_5129.contig-group-0.g.vcf.gz.tbi, called/N_5129.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-0.log jobid: 1412 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/M5672.contig-group-22.g.vcf.gz, called/M5672.contig-group-22.g.vcf.gz.tbi, called/M5672.contig-group-22.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-22.log jobid: 3521 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-22.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1927.contig-group-2.g.vcf.gz, called/N_1927.contig-group-2.g.vcf.gz.tbi, called/N_1927.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-2.log jobid: 1624 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_6490.contig-group-10.g.vcf.gz, called/N_6490.contig-group-10.g.vcf.gz.tbi, called/N_6490.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-10.log jobid: 2418 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T72.contig-group-1.g.vcf.gz, called/T72.contig-group-1.g.vcf.gz.tbi, called/T72.contig-group-1.g.done log: logs/gatk/haplotypecaller/T72.contig-group-1.log jobid: 1594 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-1.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N2005.contig-group-12.g.vcf.gz, called/N2005.contig-group-12.g.vcf.gz.tbi, called/N2005.contig-group-12.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-12.log jobid: 2563 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-12.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_2003_5409.contig-group-24.g.vcf.gz, called/N_2003_5409.contig-group-24.g.vcf.gz.tbi, called/N_2003_5409.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-24.log jobid: 3746 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T187.contig-group-16.g.vcf.gz, called/T187.contig-group-16.g.vcf.gz.tbi, called/T187.contig-group-16.g.done log: logs/gatk/haplotypecaller/T187.contig-group-16.log jobid: 3024 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-16.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1870.contig-group-23.g.vcf.gz, called/N_1870.contig-group-23.g.vcf.gz.tbi, called/N_1870.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-23.log jobid: 3637 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_8583.contig-group-18.g.vcf.gz, called/N_8583.contig-group-18.g.vcf.gz.tbi, called/N_8583.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-18.log jobid: 3202 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1158.contig-group-15.g.vcf.gz, called/N_1158.contig-group-15.g.vcf.gz.tbi, called/N_1158.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-15.log jobid: 2856 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_4843.contig-group-26.g.vcf.gz, called/N_4843.contig-group-26.g.vcf.gz.tbi, called/N_4843.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-26.log jobid: 3946 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T1483.contig-group-13.g.vcf.gz, called/T1483.contig-group-13.g.vcf.gz.tbi, called/T1483.contig-group-13.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-13.log jobid: 2729 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-13.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T190.contig-group-18.g.vcf.gz, called/T190.contig-group-18.g.vcf.gz.tbi, called/T190.contig-group-18.g.done log: logs/gatk/haplotypecaller/T190.contig-group-18.log jobid: 3219 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-18.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_102.contig-group-26.g.vcf.gz, called/N_102.contig-group-26.g.vcf.gz.tbi, called/N_102.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-26.log jobid: 3908 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_2003_5409.contig-group-13.g.vcf.gz, called/N_2003_5409.contig-group-13.g.vcf.gz.tbi, called/N_2003_5409.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-13.log jobid: 2690 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T1483.contig-group-25.g.vcf.gz, called/T1483.contig-group-25.g.vcf.gz.tbi, called/T1483.contig-group-25.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-25.log jobid: 3881 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-25.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1158.contig-group-22.g.vcf.gz, called/N_1158.contig-group-22.g.vcf.gz.tbi, called/N_1158.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-22.log jobid: 3528 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T1483.contig-group-16.g.vcf.gz, called/T1483.contig-group-16.g.vcf.gz.tbi, called/T1483.contig-group-16.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-16.log jobid: 3017 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-16.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T180.contig-group-8.g.vcf.gz, called/T180.contig-group-8.g.vcf.gz.tbi, called/T180.contig-group-8.g.done log: logs/gatk/haplotypecaller/T180.contig-group-8.log jobid: 2252 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-8.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1870.contig-group-2.g.vcf.gz, called/N_1870.contig-group-2.g.vcf.gz.tbi, called/N_1870.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-2.log jobid: 1621 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_6928.contig-group-20.g.vcf.gz, called/N_6928.contig-group-20.g.vcf.gz.tbi, called/N_6928.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-20.log jobid: 3383 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_4847.contig-group-20.g.vcf.gz, called/N_4847.contig-group-20.g.vcf.gz.tbi, called/N_4847.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-20.log jobid: 3373 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_4843.contig-group-17.g.vcf.gz, called/N_4843.contig-group-17.g.vcf.gz.tbi, called/N_4843.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-17.log jobid: 3082 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T196.contig-group-21.g.vcf.gz, called/T196.contig-group-21.g.vcf.gz.tbi, called/T196.contig-group-21.g.done log: logs/gatk/haplotypecaller/T196.contig-group-21.log jobid: 3511 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-21.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_689.contig-group-14.g.vcf.gz, called/N_689.contig-group-14.g.vcf.gz.tbi, called/N_689.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-14.log jobid: 2804 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1386.contig-group-10.g.vcf.gz, called/N_1386.contig-group-10.g.vcf.gz.tbi, called/N_1386.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-10.log jobid: 2382 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_8565.contig-group-3.g.vcf.gz, called/N_8565.contig-group-3.g.vcf.gz.tbi, called/N_8565.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-3.log jobid: 1761 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T72.contig-group-24.g.vcf.gz, called/T72.contig-group-24.g.vcf.gz.tbi, called/T72.contig-group-24.g.done log: logs/gatk/haplotypecaller/T72.contig-group-24.log jobid: 3802 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-24.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_83.contig-group-23.g.vcf.gz, called/N_83.contig-group-23.g.vcf.gz.tbi, called/N_83.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-23.log jobid: 3679 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1870.contig-group-16.g.vcf.gz, called/N_1870.contig-group-16.g.vcf.gz.tbi, called/N_1870.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-16.log jobid: 2965 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_4847.contig-group-15.g.vcf.gz, called/N_4847.contig-group-15.g.vcf.gz.tbi, called/N_4847.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-15.log jobid: 2893 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T192.contig-group-20.g.vcf.gz, called/T192.contig-group-20.g.vcf.gz.tbi, called/T192.contig-group-20.g.done log: logs/gatk/haplotypecaller/T192.contig-group-20.log jobid: 3412 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-20.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_8565.contig-group-6.g.vcf.gz, called/N_8565.contig-group-6.g.vcf.gz.tbi, called/N_8565.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-6.log jobid: 2049 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1927.contig-group-3.g.vcf.gz, called/N_1927.contig-group-3.g.vcf.gz.tbi, called/N_1927.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-3.log jobid: 1720 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_4843.contig-group-19.g.vcf.gz, called/N_4843.contig-group-19.g.vcf.gz.tbi, called/N_4843.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-19.log jobid: 3274 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1156.contig-group-8.g.vcf.gz, called/N_1156.contig-group-8.g.vcf.gz.tbi, called/N_1156.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-8.log jobid: 2182 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T1483.contig-group-5.g.vcf.gz, called/T1483.contig-group-5.g.vcf.gz.tbi, called/T1483.contig-group-5.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-5.log jobid: 1961 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-5.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_689.contig-group-21.g.vcf.gz, called/N_689.contig-group-21.g.vcf.gz.tbi, called/N_689.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-21.log jobid: 3476 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_9449.contig-group-15.g.vcf.gz, called/N_9449.contig-group-15.g.vcf.gz.tbi, called/N_9449.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-15.log jobid: 2918 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1157.contig-group-12.g.vcf.gz, called/N_1157.contig-group-12.g.vcf.gz.tbi, called/N_1157.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-12.log jobid: 2567 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_4847.contig-group-6.g.vcf.gz, called/N_4847.contig-group-6.g.vcf.gz.tbi, called/N_4847.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-6.log jobid: 2029 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1157.contig-group-26.g.vcf.gz, called/N_1157.contig-group-26.g.vcf.gz.tbi, called/N_1157.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-26.log jobid: 3911 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_6489.contig-group-14.g.vcf.gz, called/N_6489.contig-group-14.g.vcf.gz.tbi, called/N_6489.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-14.log jobid: 2801 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_83.contig-group-26.g.vcf.gz, called/N_83.contig-group-26.g.vcf.gz.tbi, called/N_83.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-26.log jobid: 3967 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T185.contig-group-17.g.vcf.gz, called/T185.contig-group-17.g.vcf.gz.tbi, called/T185.contig-group-17.g.done log: logs/gatk/haplotypecaller/T185.contig-group-17.log jobid: 3118 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-17.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1354.contig-group-22.g.vcf.gz, called/N_1354.contig-group-22.g.vcf.gz.tbi, called/N_1354.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-22.log jobid: 3531 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1934_1_1_5973.contig-group-12.g.vcf.gz, called/N_1934_1_1_5973.contig-group-12.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-12.log jobid: 2587 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_79.contig-group-15.g.vcf.gz, called/N_79.contig-group-15.g.vcf.gz.tbi, called/N_79.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-15.log jobid: 2907 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N2005.contig-group-2.g.vcf.gz, called/N2005.contig-group-2.g.vcf.gz.tbi, called/N2005.contig-group-2.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-2.log jobid: 1603 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-2.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1609.contig-group-15.g.vcf.gz, called/N_1609.contig-group-15.g.vcf.gz.tbi, called/N_1609.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-15.log jobid: 2868 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1386.contig-group-19.g.vcf.gz, called/N_1386.contig-group-19.g.vcf.gz.tbi, called/N_1386.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-19.log jobid: 3246 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1927.contig-group-4.g.vcf.gz, called/N_1927.contig-group-4.g.vcf.gz.tbi, called/N_1927.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-4.log jobid: 1816 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1992_0123.contig-group-25.g.vcf.gz, called/N_1992_0123.contig-group-25.g.vcf.gz.tbi, called/N_1992_0123.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-25.log jobid: 3837 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1158.contig-group-4.g.vcf.gz, called/N_1158.contig-group-4.g.vcf.gz.tbi, called/N_1158.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-4.log jobid: 1800 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/M5672.contig-group-11.g.vcf.gz, called/M5672.contig-group-11.g.vcf.gz.tbi, called/M5672.contig-group-11.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-11.log jobid: 2465 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-11.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T1483.contig-group-4.g.vcf.gz, called/T1483.contig-group-4.g.vcf.gz.tbi, called/T1483.contig-group-4.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-4.log jobid: 1865 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-4.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T79.contig-group-0.g.vcf.gz, called/T79.contig-group-0.g.vcf.gz.tbi, called/T79.contig-group-0.g.done log: logs/gatk/haplotypecaller/T79.contig-group-0.log jobid: 1498 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-0.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_9104.contig-group-23.g.vcf.gz, called/N_9104.contig-group-23.g.vcf.gz.tbi, called/N_9104.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-23.log jobid: 3685 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_5129.contig-group-26.g.vcf.gz, called/N_5129.contig-group-26.g.vcf.gz.tbi, called/N_5129.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-26.log jobid: 3952 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1354.contig-group-6.g.vcf.gz, called/N_1354.contig-group-6.g.vcf.gz.tbi, called/N_1354.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-6.log jobid: 1995 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1992_0123.contig-group-1.g.vcf.gz, called/N_1992_0123.contig-group-1.g.vcf.gz.tbi, called/N_1992_0123.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-1.log jobid: 1533 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/M5672.contig-group-10.g.vcf.gz, called/M5672.contig-group-10.g.vcf.gz.tbi, called/M5672.contig-group-10.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-10.log jobid: 2369 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-10.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_9449.contig-group-26.g.vcf.gz, called/N_9449.contig-group-26.g.vcf.gz.tbi, called/N_9449.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-26.log jobid: 3974 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1934_1_1_5973.contig-group-7.g.vcf.gz, called/N_1934_1_1_5973.contig-group-7.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-7.log jobid: 2107 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_102.contig-group-3.g.vcf.gz, called/N_102.contig-group-3.g.vcf.gz.tbi, called/N_102.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-3.log jobid: 1700 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T72.contig-group-18.g.vcf.gz, called/T72.contig-group-18.g.vcf.gz.tbi, called/T72.contig-group-18.g.done log: logs/gatk/haplotypecaller/T72.contig-group-18.log jobid: 3226 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-18.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_690.contig-group-3.g.vcf.gz, called/N_690.contig-group-3.g.vcf.gz.tbi, called/N_690.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-3.log jobid: 1749 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T187.contig-group-13.g.vcf.gz, called/T187.contig-group-13.g.vcf.gz.tbi, called/T187.contig-group-13.g.done log: logs/gatk/haplotypecaller/T187.contig-group-13.log jobid: 2736 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-13.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_351.contig-group-19.g.vcf.gz, called/N_351.contig-group-19.g.vcf.gz.tbi, called/N_351.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-19.log jobid: 3270 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_8583.contig-group-25.g.vcf.gz, called/N_8583.contig-group-25.g.vcf.gz.tbi, called/N_8583.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-25.log jobid: 3874 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T192.contig-group-18.g.vcf.gz, called/T192.contig-group-18.g.vcf.gz.tbi, called/T192.contig-group-18.g.done log: logs/gatk/haplotypecaller/T192.contig-group-18.log jobid: 3220 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-18.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1156.contig-group-17.g.vcf.gz, called/N_1156.contig-group-17.g.vcf.gz.tbi, called/N_1156.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-17.log jobid: 3046 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1870.contig-group-20.g.vcf.gz, called/N_1870.contig-group-20.g.vcf.gz.tbi, called/N_1870.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-20.log jobid: 3349 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_5129.contig-group-1.g.vcf.gz, called/N_5129.contig-group-1.g.vcf.gz.tbi, called/N_5129.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-1.log jobid: 1552 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1992_0123.contig-group-10.g.vcf.gz, called/N_1992_0123.contig-group-10.g.vcf.gz.tbi, called/N_1992_0123.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-10.log jobid: 2397 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1354.contig-group-15.g.vcf.gz, called/N_1354.contig-group-15.g.vcf.gz.tbi, called/N_1354.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-15.log jobid: 2859 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_79.contig-group-4.g.vcf.gz, called/N_79.contig-group-4.g.vcf.gz.tbi, called/N_79.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-4.log jobid: 1851 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_102.contig-group-8.g.vcf.gz, called/N_102.contig-group-8.g.vcf.gz.tbi, called/N_102.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-8.log jobid: 2180 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_690.contig-group-18.g.vcf.gz, called/N_690.contig-group-18.g.vcf.gz.tbi, called/N_690.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-18.log jobid: 3189 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/M5672.contig-group-7.g.vcf.gz, called/M5672.contig-group-7.g.vcf.gz.tbi, called/M5672.contig-group-7.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-7.log jobid: 2081 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-7.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_351.contig-group-18.g.vcf.gz, called/N_351.contig-group-18.g.vcf.gz.tbi, called/N_351.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-18.log jobid: 3174 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T196.contig-group-6.g.vcf.gz, called/T196.contig-group-6.g.vcf.gz.tbi, called/T196.contig-group-6.g.done log: logs/gatk/haplotypecaller/T196.contig-group-6.log jobid: 2071 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-6.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1870.contig-group-17.g.vcf.gz, called/N_1870.contig-group-17.g.vcf.gz.tbi, called/N_1870.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-17.log jobid: 3061 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/M5672.contig-group-9.g.vcf.gz, called/M5672.contig-group-9.g.vcf.gz.tbi, called/M5672.contig-group-9.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-9.log jobid: 2273 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-9.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_83.contig-group-2.g.vcf.gz, called/N_83.contig-group-2.g.vcf.gz.tbi, called/N_83.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-2.log jobid: 1663 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T1483.contig-group-12.g.vcf.gz, called/T1483.contig-group-12.g.vcf.gz.tbi, called/T1483.contig-group-12.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-12.log jobid: 2633 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-12.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T180.contig-group-11.g.vcf.gz, called/T180.contig-group-11.g.vcf.gz.tbi, called/T180.contig-group-11.g.done log: logs/gatk/haplotypecaller/T180.contig-group-11.log jobid: 2540 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-11.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T196.contig-group-10.g.vcf.gz, called/T196.contig-group-10.g.vcf.gz.tbi, called/T196.contig-group-10.g.done log: logs/gatk/haplotypecaller/T196.contig-group-10.log jobid: 2455 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-10.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_6928.contig-group-3.g.vcf.gz, called/N_6928.contig-group-3.g.vcf.gz.tbi, called/N_6928.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-3.log jobid: 1751 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_8565.contig-group-10.g.vcf.gz, called/N_8565.contig-group-10.g.vcf.gz.tbi, called/N_8565.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-10.log jobid: 2433 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T1483.contig-group-23.g.vcf.gz, called/T1483.contig-group-23.g.vcf.gz.tbi, called/T1483.contig-group-23.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-23.log jobid: 3689 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-23.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_79.contig-group-24.g.vcf.gz, called/N_79.contig-group-24.g.vcf.gz.tbi, called/N_79.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-24.log jobid: 3771 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T79.contig-group-7.g.vcf.gz, called/T79.contig-group-7.g.vcf.gz.tbi, called/T79.contig-group-7.g.done log: logs/gatk/haplotypecaller/T79.contig-group-7.log jobid: 2171 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-7.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_9104.contig-group-4.g.vcf.gz, called/N_9104.contig-group-4.g.vcf.gz.tbi, called/N_9104.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-4.log jobid: 1861 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_4843.contig-group-1.g.vcf.gz, called/N_4843.contig-group-1.g.vcf.gz.tbi, called/N_4843.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-1.log jobid: 1546 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1609.contig-group-18.g.vcf.gz, called/N_1609.contig-group-18.g.vcf.gz.tbi, called/N_1609.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-18.log jobid: 3156 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T190.contig-group-20.g.vcf.gz, called/T190.contig-group-20.g.vcf.gz.tbi, called/T190.contig-group-20.g.done log: logs/gatk/haplotypecaller/T190.contig-group-20.log jobid: 3411 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-20.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_351.contig-group-14.g.vcf.gz, called/N_351.contig-group-14.g.vcf.gz.tbi, called/N_351.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-14.log jobid: 2790 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1156.contig-group-20.g.vcf.gz, called/N_1156.contig-group-20.g.vcf.gz.tbi, called/N_1156.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-20.log jobid: 3334 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_102.contig-group-4.g.vcf.gz, called/N_102.contig-group-4.g.vcf.gz.tbi, called/N_102.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-4.log jobid: 1796 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T192.contig-group-21.g.vcf.gz, called/T192.contig-group-21.g.vcf.gz.tbi, called/T192.contig-group-21.g.done log: logs/gatk/haplotypecaller/T192.contig-group-21.log jobid: 3508 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-21.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_9104.contig-group-24.g.vcf.gz, called/N_9104.contig-group-24.g.vcf.gz.tbi, called/N_9104.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-24.log jobid: 3781 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1354.contig-group-8.g.vcf.gz, called/N_1354.contig-group-8.g.vcf.gz.tbi, called/N_1354.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-8.log jobid: 2187 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1927.contig-group-21.g.vcf.gz, called/N_1927.contig-group-21.g.vcf.gz.tbi, called/N_1927.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-21.log jobid: 3448 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1386.contig-group-24.g.vcf.gz, called/N_1386.contig-group-24.g.vcf.gz.tbi, called/N_1386.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-24.log jobid: 3726 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1157.contig-group-25.g.vcf.gz, called/N_1157.contig-group-25.g.vcf.gz.tbi, called/N_1157.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-25.log jobid: 3815 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_8171.contig-group-25.g.vcf.gz, called/N_8171.contig-group-25.g.vcf.gz.tbi, called/N_8171.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-25.log jobid: 3870 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T79.contig-group-15.g.vcf.gz, called/T79.contig-group-15.g.vcf.gz.tbi, called/T79.contig-group-15.g.done log: logs/gatk/haplotypecaller/T79.contig-group-15.log jobid: 2939 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-15.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1158.contig-group-26.g.vcf.gz, called/N_1158.contig-group-26.g.vcf.gz.tbi, called/N_1158.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-26.log jobid: 3912 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1386.contig-group-12.g.vcf.gz, called/N_1386.contig-group-12.g.vcf.gz.tbi, called/N_1386.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-12.log jobid: 2574 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_9104.contig-group-14.g.vcf.gz, called/N_9104.contig-group-14.g.vcf.gz.tbi, called/N_9104.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-14.log jobid: 2821 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1927.contig-group-23.g.vcf.gz, called/N_1927.contig-group-23.g.vcf.gz.tbi, called/N_1927.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-23.log jobid: 3640 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_102.contig-group-2.g.vcf.gz, called/N_102.contig-group-2.g.vcf.gz.tbi, called/N_102.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-2.log jobid: 1604 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T190.contig-group-25.g.vcf.gz, called/T190.contig-group-25.g.vcf.gz.tbi, called/T190.contig-group-25.g.done log: logs/gatk/haplotypecaller/T190.contig-group-25.log jobid: 3891 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-25.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1157.contig-group-10.g.vcf.gz, called/N_1157.contig-group-10.g.vcf.gz.tbi, called/N_1157.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-10.log jobid: 2375 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T185.contig-group-16.g.vcf.gz, called/T185.contig-group-16.g.vcf.gz.tbi, called/T185.contig-group-16.g.done log: logs/gatk/haplotypecaller/T185.contig-group-16.log jobid: 3022 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-16.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T192.contig-group-7.g.vcf.gz, called/T192.contig-group-7.g.vcf.gz.tbi, called/T192.contig-group-7.g.done log: logs/gatk/haplotypecaller/T192.contig-group-7.log jobid: 2164 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-7.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1927.contig-group-17.g.vcf.gz, called/N_1927.contig-group-17.g.vcf.gz.tbi, called/N_1927.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-17.log jobid: 3064 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1934_1_1_5973.contig-group-23.g.vcf.gz, called/N_1934_1_1_5973.contig-group-23.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-23.log jobid: 3643 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1609.contig-group-9.g.vcf.gz, called/N_1609.contig-group-9.g.vcf.gz.tbi, called/N_1609.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-9.log jobid: 2292 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1934_1_1_5973.contig-group-16.g.vcf.gz, called/N_1934_1_1_5973.contig-group-16.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-16.log jobid: 2971 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1992_0123.contig-group-0.g.vcf.gz, called/N_1992_0123.contig-group-0.g.vcf.gz.tbi, called/N_1992_0123.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-0.log jobid: 1374 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1354.contig-group-11.g.vcf.gz, called/N_1354.contig-group-11.g.vcf.gz.tbi, called/N_1354.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-11.log jobid: 2475 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_8583.contig-group-24.g.vcf.gz, called/N_8583.contig-group-24.g.vcf.gz.tbi, called/N_8583.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-24.log jobid: 3778 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_2003_5409.contig-group-4.g.vcf.gz, called/N_2003_5409.contig-group-4.g.vcf.gz.tbi, called/N_2003_5409.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-4.log jobid: 1826 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1992_0123.contig-group-13.g.vcf.gz, called/N_1992_0123.contig-group-13.g.vcf.gz.tbi, called/N_1992_0123.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-13.log jobid: 2685 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_351.contig-group-6.g.vcf.gz, called/N_351.contig-group-6.g.vcf.gz.tbi, called/N_351.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-6.log jobid: 2022 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T72.contig-group-25.g.vcf.gz, called/T72.contig-group-25.g.vcf.gz.tbi, called/T72.contig-group-25.g.done log: logs/gatk/haplotypecaller/T72.contig-group-25.log jobid: 3898 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-25.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T1483.contig-group-6.g.vcf.gz, called/T1483.contig-group-6.g.vcf.gz.tbi, called/T1483.contig-group-6.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-6.log jobid: 2057 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-6.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_6489.contig-group-26.g.vcf.gz, called/N_6489.contig-group-26.g.vcf.gz.tbi, called/N_6489.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-26.log jobid: 3953 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T190.contig-group-11.g.vcf.gz, called/T190.contig-group-11.g.vcf.gz.tbi, called/T190.contig-group-11.g.done log: logs/gatk/haplotypecaller/T190.contig-group-11.log jobid: 2547 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-11.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_9449.contig-group-5.g.vcf.gz, called/N_9449.contig-group-5.g.vcf.gz.tbi, called/N_9449.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-5.log jobid: 1958 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1934_1_1_5973.contig-group-26.g.vcf.gz, called/N_1934_1_1_5973.contig-group-26.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-26.log jobid: 3931 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_79.contig-group-13.g.vcf.gz, called/N_79.contig-group-13.g.vcf.gz.tbi, called/N_79.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-13.log jobid: 2715 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_4843.contig-group-16.g.vcf.gz, called/N_4843.contig-group-16.g.vcf.gz.tbi, called/N_4843.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-16.log jobid: 2986 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1870.contig-group-10.g.vcf.gz, called/N_1870.contig-group-10.g.vcf.gz.tbi, called/N_1870.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-10.log jobid: 2389 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_690.contig-group-20.g.vcf.gz, called/N_690.contig-group-20.g.vcf.gz.tbi, called/N_690.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-20.log jobid: 3381 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_689.contig-group-2.g.vcf.gz, called/N_689.contig-group-2.g.vcf.gz.tbi, called/N_689.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-2.log jobid: 1652 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T196.contig-group-4.g.vcf.gz, called/T196.contig-group-4.g.vcf.gz.tbi, called/T196.contig-group-4.g.done log: logs/gatk/haplotypecaller/T196.contig-group-4.log jobid: 1879 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-4.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T185.contig-group-26.g.vcf.gz, called/T185.contig-group-26.g.vcf.gz.tbi, called/T185.contig-group-26.g.done log: logs/gatk/haplotypecaller/T185.contig-group-26.log jobid: 3982 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-26.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T185.contig-group-23.g.vcf.gz, called/T185.contig-group-23.g.vcf.gz.tbi, called/T185.contig-group-23.g.done log: logs/gatk/haplotypecaller/T185.contig-group-23.log jobid: 3694 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-23.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1158.contig-group-24.g.vcf.gz, called/N_1158.contig-group-24.g.vcf.gz.tbi, called/N_1158.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-24.log jobid: 3720 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1992_0123.contig-group-7.g.vcf.gz, called/N_1992_0123.contig-group-7.g.vcf.gz.tbi, called/N_1992_0123.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-7.log jobid: 2109 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_8583.contig-group-8.g.vcf.gz, called/N_8583.contig-group-8.g.vcf.gz.tbi, called/N_8583.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-8.log jobid: 2242 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1157.contig-group-17.g.vcf.gz, called/N_1157.contig-group-17.g.vcf.gz.tbi, called/N_1157.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-17.log jobid: 3047 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T1483.contig-group-24.g.vcf.gz, called/T1483.contig-group-24.g.vcf.gz.tbi, called/T1483.contig-group-24.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-24.log jobid: 3785 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-24.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_8583.contig-group-0.g.vcf.gz, called/N_8583.contig-group-0.g.vcf.gz.tbi, called/N_8583.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-0.log jobid: 1448 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_690.contig-group-15.g.vcf.gz, called/N_690.contig-group-15.g.vcf.gz.tbi, called/N_690.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-15.log jobid: 2901 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_690.contig-group-4.g.vcf.gz, called/N_690.contig-group-4.g.vcf.gz.tbi, called/N_690.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-4.log jobid: 1845 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_6490.contig-group-21.g.vcf.gz, called/N_6490.contig-group-21.g.vcf.gz.tbi, called/N_6490.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-21.log jobid: 3474 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1386.contig-group-2.g.vcf.gz, called/N_1386.contig-group-2.g.vcf.gz.tbi, called/N_1386.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-2.log jobid: 1614 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T196.contig-group-23.g.vcf.gz, called/T196.contig-group-23.g.vcf.gz.tbi, called/T196.contig-group-23.g.done log: logs/gatk/haplotypecaller/T196.contig-group-23.log jobid: 3703 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-23.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_79.contig-group-8.g.vcf.gz, called/N_79.contig-group-8.g.vcf.gz.tbi, called/N_79.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-8.log jobid: 2235 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T79.contig-group-2.g.vcf.gz, called/T79.contig-group-2.g.vcf.gz.tbi, called/T79.contig-group-2.g.done log: logs/gatk/haplotypecaller/T79.contig-group-2.log jobid: 1691 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-2.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_6489.contig-group-0.g.vcf.gz, called/N_6489.contig-group-0.g.vcf.gz.tbi, called/N_6489.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-0.log jobid: 1414 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1354.contig-group-10.g.vcf.gz, called/N_1354.contig-group-10.g.vcf.gz.tbi, called/N_1354.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-10.log jobid: 2379 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_4847.contig-group-13.g.vcf.gz, called/N_4847.contig-group-13.g.vcf.gz.tbi, called/N_4847.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-13.log jobid: 2701 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T180.contig-group-5.g.vcf.gz, called/T180.contig-group-5.g.vcf.gz.tbi, called/T180.contig-group-5.g.done log: logs/gatk/haplotypecaller/T180.contig-group-5.log jobid: 1964 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-5.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1927.contig-group-5.g.vcf.gz, called/N_1927.contig-group-5.g.vcf.gz.tbi, called/N_1927.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-5.log jobid: 1912 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1992_0123.contig-group-22.g.vcf.gz, called/N_1992_0123.contig-group-22.g.vcf.gz.tbi, called/N_1992_0123.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-22.log jobid: 3549 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T185.contig-group-22.g.vcf.gz, called/T185.contig-group-22.g.vcf.gz.tbi, called/T185.contig-group-22.g.done log: logs/gatk/haplotypecaller/T185.contig-group-22.log jobid: 3598 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-22.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1927.contig-group-10.g.vcf.gz, called/N_1927.contig-group-10.g.vcf.gz.tbi, called/N_1927.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-10.log jobid: 2392 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/M5672.contig-group-0.g.vcf.gz, called/M5672.contig-group-0.g.vcf.gz.tbi, called/M5672.contig-group-0.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-0.log jobid: 1318 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-0.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_9104.contig-group-11.g.vcf.gz, called/N_9104.contig-group-11.g.vcf.gz.tbi, called/N_9104.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-11.log jobid: 2533 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T79.contig-group-22.g.vcf.gz, called/T79.contig-group-22.g.vcf.gz.tbi, called/T79.contig-group-22.g.done log: logs/gatk/haplotypecaller/T79.contig-group-22.log jobid: 3611 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-22.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N2005.contig-group-13.g.vcf.gz, called/N2005.contig-group-13.g.vcf.gz.tbi, called/N2005.contig-group-13.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-13.log jobid: 2659 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-13.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T196.contig-group-26.g.vcf.gz, called/T196.contig-group-26.g.vcf.gz.tbi, called/T196.contig-group-26.g.done log: logs/gatk/haplotypecaller/T196.contig-group-26.log jobid: 3991 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-26.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1870.contig-group-7.g.vcf.gz, called/N_1870.contig-group-7.g.vcf.gz.tbi, called/N_1870.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-7.log jobid: 2101 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1156.contig-group-3.g.vcf.gz, called/N_1156.contig-group-3.g.vcf.gz.tbi, called/N_1156.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-3.log jobid: 1702 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_9104.contig-group-5.g.vcf.gz, called/N_9104.contig-group-5.g.vcf.gz.tbi, called/N_9104.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-5.log jobid: 1957 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1156.contig-group-19.g.vcf.gz, called/N_1156.contig-group-19.g.vcf.gz.tbi, called/N_1156.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-19.log jobid: 3238 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_8583.contig-group-10.g.vcf.gz, called/N_8583.contig-group-10.g.vcf.gz.tbi, called/N_8583.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-10.log jobid: 2434 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_4847.contig-group-3.g.vcf.gz, called/N_4847.contig-group-3.g.vcf.gz.tbi, called/N_4847.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-3.log jobid: 1741 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T1483.contig-group-0.g.vcf.gz, called/T1483.contig-group-0.g.vcf.gz.tbi, called/T1483.contig-group-0.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-0.log jobid: 1462 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-0.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T180.contig-group-19.g.vcf.gz, called/T180.contig-group-19.g.vcf.gz.tbi, called/T180.contig-group-19.g.done log: logs/gatk/haplotypecaller/T180.contig-group-19.log jobid: 3308 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-19.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_8565.contig-group-20.g.vcf.gz, called/N_8565.contig-group-20.g.vcf.gz.tbi, called/N_8565.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-20.log jobid: 3393 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_102.contig-group-20.g.vcf.gz, called/N_102.contig-group-20.g.vcf.gz.tbi, called/N_102.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-20.log jobid: 3332 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1927.contig-group-24.g.vcf.gz, called/N_1927.contig-group-24.g.vcf.gz.tbi, called/N_1927.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-24.log jobid: 3736 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T192.contig-group-0.g.vcf.gz, called/T192.contig-group-0.g.vcf.gz.tbi, called/T192.contig-group-0.g.done log: logs/gatk/haplotypecaller/T192.contig-group-0.log jobid: 1484 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-0.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_79.contig-group-20.g.vcf.gz, called/N_79.contig-group-20.g.vcf.gz.tbi, called/N_79.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-20.log jobid: 3387 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1870.contig-group-21.g.vcf.gz, called/N_1870.contig-group-21.g.vcf.gz.tbi, called/N_1870.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-21.log jobid: 3445 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_4843.contig-group-3.g.vcf.gz, called/N_4843.contig-group-3.g.vcf.gz.tbi, called/N_4843.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-3.log jobid: 1738 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N2005.contig-group-19.g.vcf.gz, called/N2005.contig-group-19.g.vcf.gz.tbi, called/N2005.contig-group-19.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-19.log jobid: 3235 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-19.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1354.contig-group-14.g.vcf.gz, called/N_1354.contig-group-14.g.vcf.gz.tbi, called/N_1354.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-14.log jobid: 2763 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_5129.contig-group-4.g.vcf.gz, called/N_5129.contig-group-4.g.vcf.gz.tbi, called/N_5129.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-4.log jobid: 1840 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_83.contig-group-6.g.vcf.gz, called/N_83.contig-group-6.g.vcf.gz.tbi, called/N_83.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-6.log jobid: 2047 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1934_1_1_5973.contig-group-19.g.vcf.gz, called/N_1934_1_1_5973.contig-group-19.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-19.log jobid: 3259 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_690.contig-group-25.g.vcf.gz, called/N_690.contig-group-25.g.vcf.gz.tbi, called/N_690.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-25.log jobid: 3861 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_351.contig-group-25.g.vcf.gz, called/N_351.contig-group-25.g.vcf.gz.tbi, called/N_351.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-25.log jobid: 3846 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1870.contig-group-8.g.vcf.gz, called/N_1870.contig-group-8.g.vcf.gz.tbi, called/N_1870.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-8.log jobid: 2197 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_689.contig-group-12.g.vcf.gz, called/N_689.contig-group-12.g.vcf.gz.tbi, called/N_689.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-12.log jobid: 2612 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_5129.contig-group-17.g.vcf.gz, called/N_5129.contig-group-17.g.vcf.gz.tbi, called/N_5129.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-17.log jobid: 3088 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T180.contig-group-23.g.vcf.gz, called/T180.contig-group-23.g.vcf.gz.tbi, called/T180.contig-group-23.g.done log: logs/gatk/haplotypecaller/T180.contig-group-23.log jobid: 3692 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-23.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_351.contig-group-0.g.vcf.gz, called/N_351.contig-group-0.g.vcf.gz.tbi, called/N_351.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-0.log jobid: 1392 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_4847.contig-group-25.g.vcf.gz, called/N_4847.contig-group-25.g.vcf.gz.tbi, called/N_4847.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-25.log jobid: 3853 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1156.contig-group-22.g.vcf.gz, called/N_1156.contig-group-22.g.vcf.gz.tbi, called/N_1156.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-22.log jobid: 3526 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1386.contig-group-26.g.vcf.gz, called/N_1386.contig-group-26.g.vcf.gz.tbi, called/N_1386.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-26.log jobid: 3918 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_6928.contig-group-10.g.vcf.gz, called/N_6928.contig-group-10.g.vcf.gz.tbi, called/N_6928.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-10.log jobid: 2423 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_5129.contig-group-2.g.vcf.gz, called/N_5129.contig-group-2.g.vcf.gz.tbi, called/N_5129.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-2.log jobid: 1648 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_102.contig-group-17.g.vcf.gz, called/N_102.contig-group-17.g.vcf.gz.tbi, called/N_102.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-17.log jobid: 3044 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T72.contig-group-11.g.vcf.gz, called/T72.contig-group-11.g.vcf.gz.tbi, called/T72.contig-group-11.g.done log: logs/gatk/haplotypecaller/T72.contig-group-11.log jobid: 2554 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-11.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1609.contig-group-16.g.vcf.gz, called/N_1609.contig-group-16.g.vcf.gz.tbi, called/N_1609.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-16.log jobid: 2964 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_5129.contig-group-22.g.vcf.gz, called/N_5129.contig-group-22.g.vcf.gz.tbi, called/N_5129.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-22.log jobid: 3568 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T180.contig-group-6.g.vcf.gz, called/T180.contig-group-6.g.vcf.gz.tbi, called/T180.contig-group-6.g.done log: logs/gatk/haplotypecaller/T180.contig-group-6.log jobid: 2060 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-6.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_83.contig-group-14.g.vcf.gz, called/N_83.contig-group-14.g.vcf.gz.tbi, called/N_83.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-14.log jobid: 2815 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_4847.contig-group-23.g.vcf.gz, called/N_4847.contig-group-23.g.vcf.gz.tbi, called/N_4847.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-23.log jobid: 3661 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T187.contig-group-0.g.vcf.gz, called/T187.contig-group-0.g.vcf.gz.tbi, called/T187.contig-group-0.g.done log: logs/gatk/haplotypecaller/T187.contig-group-0.log jobid: 1476 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-0.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1934_1_1_5973.contig-group-20.g.vcf.gz, called/N_1934_1_1_5973.contig-group-20.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-20.log jobid: 3355 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_8583.contig-group-12.g.vcf.gz, called/N_8583.contig-group-12.g.vcf.gz.tbi, called/N_8583.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-12.log jobid: 2626 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T79.contig-group-11.g.vcf.gz, called/T79.contig-group-11.g.vcf.gz.tbi, called/T79.contig-group-11.g.done log: logs/gatk/haplotypecaller/T79.contig-group-11.log jobid: 2555 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-11.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_8171.contig-group-10.g.vcf.gz, called/N_8171.contig-group-10.g.vcf.gz.tbi, called/N_8171.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-10.log jobid: 2430 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_6928.contig-group-6.g.vcf.gz, called/N_6928.contig-group-6.g.vcf.gz.tbi, called/N_6928.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-6.log jobid: 2039 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1992_0123.contig-group-15.g.vcf.gz, called/N_1992_0123.contig-group-15.g.vcf.gz.tbi, called/N_1992_0123.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-15.log jobid: 2877 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_2003_5409.contig-group-15.g.vcf.gz, called/N_2003_5409.contig-group-15.g.vcf.gz.tbi, called/N_2003_5409.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-15.log jobid: 2882 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_8171.contig-group-14.g.vcf.gz, called/N_8171.contig-group-14.g.vcf.gz.tbi, called/N_8171.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-14.log jobid: 2814 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_4847.contig-group-26.g.vcf.gz, called/N_4847.contig-group-26.g.vcf.gz.tbi, called/N_4847.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-26.log jobid: 3949 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1992_0123.contig-group-3.g.vcf.gz, called/N_1992_0123.contig-group-3.g.vcf.gz.tbi, called/N_1992_0123.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-3.log jobid: 1725 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_690.contig-group-2.g.vcf.gz, called/N_690.contig-group-2.g.vcf.gz.tbi, called/N_690.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-2.log jobid: 1653 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T180.contig-group-4.g.vcf.gz, called/T180.contig-group-4.g.vcf.gz.tbi, called/T180.contig-group-4.g.done log: logs/gatk/haplotypecaller/T180.contig-group-4.log jobid: 1868 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-4.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_351.contig-group-23.g.vcf.gz, called/N_351.contig-group-23.g.vcf.gz.tbi, called/N_351.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-23.log jobid: 3654 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_79.contig-group-3.g.vcf.gz, called/N_79.contig-group-3.g.vcf.gz.tbi, called/N_79.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-3.log jobid: 1755 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_9449.contig-group-16.g.vcf.gz, called/N_9449.contig-group-16.g.vcf.gz.tbi, called/N_9449.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-16.log jobid: 3014 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T185.contig-group-14.g.vcf.gz, called/T185.contig-group-14.g.vcf.gz.tbi, called/T185.contig-group-14.g.done log: logs/gatk/haplotypecaller/T185.contig-group-14.log jobid: 2830 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-14.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_9104.contig-group-22.g.vcf.gz, called/N_9104.contig-group-22.g.vcf.gz.tbi, called/N_9104.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-22.log jobid: 3589 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T72.contig-group-5.g.vcf.gz, called/T72.contig-group-5.g.vcf.gz.tbi, called/T72.contig-group-5.g.done log: logs/gatk/haplotypecaller/T72.contig-group-5.log jobid: 1978 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-5.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_4843.contig-group-9.g.vcf.gz, called/N_4843.contig-group-9.g.vcf.gz.tbi, called/N_4843.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-9.log jobid: 2314 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1354.contig-group-4.g.vcf.gz, called/N_1354.contig-group-4.g.vcf.gz.tbi, called/N_1354.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-4.log jobid: 1803 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T1483.contig-group-19.g.vcf.gz, called/T1483.contig-group-19.g.vcf.gz.tbi, called/T1483.contig-group-19.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-19.log jobid: 3305 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-19.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_689.contig-group-10.g.vcf.gz, called/N_689.contig-group-10.g.vcf.gz.tbi, called/N_689.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-10.log jobid: 2420 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_4847.contig-group-18.g.vcf.gz, called/N_4847.contig-group-18.g.vcf.gz.tbi, called/N_4847.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-18.log jobid: 3181 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T187.contig-group-15.g.vcf.gz, called/T187.contig-group-15.g.vcf.gz.tbi, called/T187.contig-group-15.g.done log: logs/gatk/haplotypecaller/T187.contig-group-15.log jobid: 2928 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-15.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_689.contig-group-18.g.vcf.gz, called/N_689.contig-group-18.g.vcf.gz.tbi, called/N_689.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-18.log jobid: 3188 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_6928.contig-group-7.g.vcf.gz, called/N_6928.contig-group-7.g.vcf.gz.tbi, called/N_6928.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-7.log jobid: 2135 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_4843.contig-group-12.g.vcf.gz, called/N_4843.contig-group-12.g.vcf.gz.tbi, called/N_4843.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-12.log jobid: 2602 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_79.contig-group-6.g.vcf.gz, called/N_79.contig-group-6.g.vcf.gz.tbi, called/N_79.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-6.log jobid: 2043 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_4847.contig-group-0.g.vcf.gz, called/N_4847.contig-group-0.g.vcf.gz.tbi, called/N_4847.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-0.log jobid: 1406 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_6928.contig-group-12.g.vcf.gz, called/N_6928.contig-group-12.g.vcf.gz.tbi, called/N_6928.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-12.log jobid: 2615 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_2003_5409.contig-group-23.g.vcf.gz, called/N_2003_5409.contig-group-23.g.vcf.gz.tbi, called/N_2003_5409.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-23.log jobid: 3650 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T187.contig-group-3.g.vcf.gz, called/T187.contig-group-3.g.vcf.gz.tbi, called/T187.contig-group-3.g.done log: logs/gatk/haplotypecaller/T187.contig-group-3.log jobid: 1776 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-3.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T72.contig-group-20.g.vcf.gz, called/T72.contig-group-20.g.vcf.gz.tbi, called/T72.contig-group-20.g.done log: logs/gatk/haplotypecaller/T72.contig-group-20.log jobid: 3418 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-20.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_689.contig-group-16.g.vcf.gz, called/N_689.contig-group-16.g.vcf.gz.tbi, called/N_689.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-16.log jobid: 2996 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_2003_5409.contig-group-6.g.vcf.gz, called/N_2003_5409.contig-group-6.g.vcf.gz.tbi, called/N_2003_5409.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-6.log jobid: 2018 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_9449.contig-group-0.g.vcf.gz, called/N_9449.contig-group-0.g.vcf.gz.tbi, called/N_9449.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-0.log jobid: 1456 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1156.contig-group-0.g.vcf.gz, called/N_1156.contig-group-0.g.vcf.gz.tbi, called/N_1156.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-0.log jobid: 1328 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T1483.contig-group-15.g.vcf.gz, called/T1483.contig-group-15.g.vcf.gz.tbi, called/T1483.contig-group-15.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-15.log jobid: 2921 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-15.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T72.contig-group-6.g.vcf.gz, called/T72.contig-group-6.g.vcf.gz.tbi, called/T72.contig-group-6.g.done log: logs/gatk/haplotypecaller/T72.contig-group-6.log jobid: 2074 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-6.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T72.contig-group-2.g.vcf.gz, called/T72.contig-group-2.g.vcf.gz.tbi, called/T72.contig-group-2.g.done log: logs/gatk/haplotypecaller/T72.contig-group-2.log jobid: 1690 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-2.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1927.contig-group-16.g.vcf.gz, called/N_1927.contig-group-16.g.vcf.gz.tbi, called/N_1927.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-16.log jobid: 2968 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_6928.contig-group-23.g.vcf.gz, called/N_6928.contig-group-23.g.vcf.gz.tbi, called/N_6928.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-23.log jobid: 3671 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_79.contig-group-1.g.vcf.gz, called/N_79.contig-group-1.g.vcf.gz.tbi, called/N_79.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-1.log jobid: 1563 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1386.contig-group-15.g.vcf.gz, called/N_1386.contig-group-15.g.vcf.gz.tbi, called/N_1386.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-15.log jobid: 2862 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1156.contig-group-9.g.vcf.gz, called/N_1156.contig-group-9.g.vcf.gz.tbi, called/N_1156.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-9.log jobid: 2278 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T79.contig-group-12.g.vcf.gz, called/T79.contig-group-12.g.vcf.gz.tbi, called/T79.contig-group-12.g.done log: logs/gatk/haplotypecaller/T79.contig-group-12.log jobid: 2651 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-12.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_9104.contig-group-19.g.vcf.gz, called/N_9104.contig-group-19.g.vcf.gz.tbi, called/N_9104.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-19.log jobid: 3301 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1157.contig-group-14.g.vcf.gz, called/N_1157.contig-group-14.g.vcf.gz.tbi, called/N_1157.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-14.log jobid: 2759 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T72.contig-group-17.g.vcf.gz, called/T72.contig-group-17.g.vcf.gz.tbi, called/T72.contig-group-17.g.done log: logs/gatk/haplotypecaller/T72.contig-group-17.log jobid: 3130 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-17.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_6490.contig-group-15.g.vcf.gz, called/N_6490.contig-group-15.g.vcf.gz.tbi, called/N_6490.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-15.log jobid: 2898 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_5129.contig-group-24.g.vcf.gz, called/N_5129.contig-group-24.g.vcf.gz.tbi, called/N_5129.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-24.log jobid: 3760 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T72.contig-group-21.g.vcf.gz, called/T72.contig-group-21.g.vcf.gz.tbi, called/T72.contig-group-21.g.done log: logs/gatk/haplotypecaller/T72.contig-group-21.log jobid: 3514 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-21.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/M5672.contig-group-18.g.vcf.gz, called/M5672.contig-group-18.g.vcf.gz.tbi, called/M5672.contig-group-18.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-18.log jobid: 3137 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-18.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T192.contig-group-16.g.vcf.gz, called/T192.contig-group-16.g.vcf.gz.tbi, called/T192.contig-group-16.g.done log: logs/gatk/haplotypecaller/T192.contig-group-16.log jobid: 3028 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-16.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T1483.contig-group-21.g.vcf.gz, called/T1483.contig-group-21.g.vcf.gz.tbi, called/T1483.contig-group-21.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-21.log jobid: 3497 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-21.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1609.contig-group-12.g.vcf.gz, called/N_1609.contig-group-12.g.vcf.gz.tbi, called/N_1609.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-12.log jobid: 2580 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_2003_5409.contig-group-22.g.vcf.gz, called/N_2003_5409.contig-group-22.g.vcf.gz.tbi, called/N_2003_5409.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-22.log jobid: 3554 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_9449.contig-group-14.g.vcf.gz, called/N_9449.contig-group-14.g.vcf.gz.tbi, called/N_9449.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-14.log jobid: 2822 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1156.contig-group-26.g.vcf.gz, called/N_1156.contig-group-26.g.vcf.gz.tbi, called/N_1156.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-26.log jobid: 3910 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_351.contig-group-5.g.vcf.gz, called/N_351.contig-group-5.g.vcf.gz.tbi, called/N_351.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-5.log jobid: 1926 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1992_0123.contig-group-12.g.vcf.gz, called/N_1992_0123.contig-group-12.g.vcf.gz.tbi, called/N_1992_0123.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-12.log jobid: 2589 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_2003_5409.contig-group-18.g.vcf.gz, called/N_2003_5409.contig-group-18.g.vcf.gz.tbi, called/N_2003_5409.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-18.log jobid: 3170 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1934_1_1_5973.contig-group-13.g.vcf.gz, called/N_1934_1_1_5973.contig-group-13.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-13.log jobid: 2683 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T72.contig-group-13.g.vcf.gz, called/T72.contig-group-13.g.vcf.gz.tbi, called/T72.contig-group-13.g.done log: logs/gatk/haplotypecaller/T72.contig-group-13.log jobid: 2746 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-13.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_9104.contig-group-25.g.vcf.gz, called/N_9104.contig-group-25.g.vcf.gz.tbi, called/N_9104.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-25.log jobid: 3877 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1992_0123.contig-group-21.g.vcf.gz, called/N_1992_0123.contig-group-21.g.vcf.gz.tbi, called/N_1992_0123.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-21.log jobid: 3453 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T185.contig-group-11.g.vcf.gz, called/T185.contig-group-11.g.vcf.gz.tbi, called/T185.contig-group-11.g.done log: logs/gatk/haplotypecaller/T185.contig-group-11.log jobid: 2542 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-11.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_6489.contig-group-1.g.vcf.gz, called/N_6489.contig-group-1.g.vcf.gz.tbi, called/N_6489.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-1.log jobid: 1553 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1156.contig-group-2.g.vcf.gz, called/N_1156.contig-group-2.g.vcf.gz.tbi, called/N_1156.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-2.log jobid: 1606 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_351.contig-group-17.g.vcf.gz, called/N_351.contig-group-17.g.vcf.gz.tbi, called/N_351.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-17.log jobid: 3078 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N2005.contig-group-16.g.vcf.gz, called/N2005.contig-group-16.g.vcf.gz.tbi, called/N2005.contig-group-16.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-16.log jobid: 2947 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-16.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T196.contig-group-19.g.vcf.gz, called/T196.contig-group-19.g.vcf.gz.tbi, called/T196.contig-group-19.g.done log: logs/gatk/haplotypecaller/T196.contig-group-19.log jobid: 3319 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-19.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T79.contig-group-4.g.vcf.gz, called/T79.contig-group-4.g.vcf.gz.tbi, called/T79.contig-group-4.g.done log: logs/gatk/haplotypecaller/T79.contig-group-4.log jobid: 1883 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-4.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1609.contig-group-2.g.vcf.gz, called/N_1609.contig-group-2.g.vcf.gz.tbi, called/N_1609.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-2.log jobid: 1620 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N2005.contig-group-4.g.vcf.gz, called/N2005.contig-group-4.g.vcf.gz.tbi, called/N2005.contig-group-4.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-4.log jobid: 1795 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-4.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_8565.contig-group-9.g.vcf.gz, called/N_8565.contig-group-9.g.vcf.gz.tbi, called/N_8565.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-9.log jobid: 2337 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_83.contig-group-7.g.vcf.gz, called/N_83.contig-group-7.g.vcf.gz.tbi, called/N_83.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-7.log jobid: 2143 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_8171.contig-group-8.g.vcf.gz, called/N_8171.contig-group-8.g.vcf.gz.tbi, called/N_8171.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-8.log jobid: 2238 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_2003_5409.contig-group-3.g.vcf.gz, called/N_2003_5409.contig-group-3.g.vcf.gz.tbi, called/N_2003_5409.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-3.log jobid: 1730 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1927.contig-group-26.g.vcf.gz, called/N_1927.contig-group-26.g.vcf.gz.tbi, called/N_1927.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-26.log jobid: 3928 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_83.contig-group-3.g.vcf.gz, called/N_83.contig-group-3.g.vcf.gz.tbi, called/N_83.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-3.log jobid: 1759 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_4847.contig-group-4.g.vcf.gz, called/N_4847.contig-group-4.g.vcf.gz.tbi, called/N_4847.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-4.log jobid: 1837 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T190.contig-group-16.g.vcf.gz, called/T190.contig-group-16.g.vcf.gz.tbi, called/T190.contig-group-16.g.done log: logs/gatk/haplotypecaller/T190.contig-group-16.log jobid: 3027 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-16.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T196.contig-group-14.g.vcf.gz, called/T196.contig-group-14.g.vcf.gz.tbi, called/T196.contig-group-14.g.done log: logs/gatk/haplotypecaller/T196.contig-group-14.log jobid: 2839 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-14.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_83.contig-group-10.g.vcf.gz, called/N_83.contig-group-10.g.vcf.gz.tbi, called/N_83.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-10.log jobid: 2431 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_6490.contig-group-17.g.vcf.gz, called/N_6490.contig-group-17.g.vcf.gz.tbi, called/N_6490.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-17.log jobid: 3090 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T187.contig-group-19.g.vcf.gz, called/T187.contig-group-19.g.vcf.gz.tbi, called/T187.contig-group-19.g.done log: logs/gatk/haplotypecaller/T187.contig-group-19.log jobid: 3312 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-19.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_6489.contig-group-24.g.vcf.gz, called/N_6489.contig-group-24.g.vcf.gz.tbi, called/N_6489.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-24.log jobid: 3761 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T72.contig-group-3.g.vcf.gz, called/T72.contig-group-3.g.vcf.gz.tbi, called/T72.contig-group-3.g.done log: logs/gatk/haplotypecaller/T72.contig-group-3.log jobid: 1786 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-3.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_83.contig-group-18.g.vcf.gz, called/N_83.contig-group-18.g.vcf.gz.tbi, called/N_83.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-18.log jobid: 3199 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_83.contig-group-21.g.vcf.gz, called/N_83.contig-group-21.g.vcf.gz.tbi, called/N_83.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-21.log jobid: 3487 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_8583.contig-group-11.g.vcf.gz, called/N_8583.contig-group-11.g.vcf.gz.tbi, called/N_8583.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-11.log jobid: 2530 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_6490.contig-group-20.g.vcf.gz, called/N_6490.contig-group-20.g.vcf.gz.tbi, called/N_6490.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-20.log jobid: 3378 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T196.contig-group-20.g.vcf.gz, called/T196.contig-group-20.g.vcf.gz.tbi, called/T196.contig-group-20.g.done log: logs/gatk/haplotypecaller/T196.contig-group-20.log jobid: 3415 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-20.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_8565.contig-group-12.g.vcf.gz, called/N_8565.contig-group-12.g.vcf.gz.tbi, called/N_8565.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-12.log jobid: 2625 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T190.contig-group-17.g.vcf.gz, called/T190.contig-group-17.g.vcf.gz.tbi, called/T190.contig-group-17.g.done log: logs/gatk/haplotypecaller/T190.contig-group-17.log jobid: 3123 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-17.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_690.contig-group-7.g.vcf.gz, called/N_690.contig-group-7.g.vcf.gz.tbi, called/N_690.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-7.log jobid: 2133 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_689.contig-group-11.g.vcf.gz, called/N_689.contig-group-11.g.vcf.gz.tbi, called/N_689.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-11.log jobid: 2516 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1386.contig-group-3.g.vcf.gz, called/N_1386.contig-group-3.g.vcf.gz.tbi, called/N_1386.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-3.log jobid: 1710 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/M5672.contig-group-13.g.vcf.gz, called/M5672.contig-group-13.g.vcf.gz.tbi, called/M5672.contig-group-13.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-13.log jobid: 2657 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-13.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1157.contig-group-23.g.vcf.gz, called/N_1157.contig-group-23.g.vcf.gz.tbi, called/N_1157.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-23.log jobid: 3623 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T196.contig-group-2.g.vcf.gz, called/T196.contig-group-2.g.vcf.gz.tbi, called/T196.contig-group-2.g.done log: logs/gatk/haplotypecaller/T196.contig-group-2.log jobid: 1687 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-2.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T190.contig-group-9.g.vcf.gz, called/T190.contig-group-9.g.vcf.gz.tbi, called/T190.contig-group-9.g.done log: logs/gatk/haplotypecaller/T190.contig-group-9.log jobid: 2355 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-9.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_8583.contig-group-13.g.vcf.gz, called/N_8583.contig-group-13.g.vcf.gz.tbi, called/N_8583.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-13.log jobid: 2722 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_351.contig-group-24.g.vcf.gz, called/N_351.contig-group-24.g.vcf.gz.tbi, called/N_351.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-24.log jobid: 3750 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1609.contig-group-21.g.vcf.gz, called/N_1609.contig-group-21.g.vcf.gz.tbi, called/N_1609.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-21.log jobid: 3444 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1156.contig-group-7.g.vcf.gz, called/N_1156.contig-group-7.g.vcf.gz.tbi, called/N_1156.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-7.log jobid: 2086 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_5129.contig-group-20.g.vcf.gz, called/N_5129.contig-group-20.g.vcf.gz.tbi, called/N_5129.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-20.log jobid: 3376 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1870.contig-group-11.g.vcf.gz, called/N_1870.contig-group-11.g.vcf.gz.tbi, called/N_1870.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-11.log jobid: 2485 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1156.contig-group-16.g.vcf.gz, called/N_1156.contig-group-16.g.vcf.gz.tbi, called/N_1156.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-16.log jobid: 2950 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_8565.contig-group-8.g.vcf.gz, called/N_8565.contig-group-8.g.vcf.gz.tbi, called/N_8565.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-8.log jobid: 2241 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1609.contig-group-26.g.vcf.gz, called/N_1609.contig-group-26.g.vcf.gz.tbi, called/N_1609.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-26.log jobid: 3924 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1609.contig-group-11.g.vcf.gz, called/N_1609.contig-group-11.g.vcf.gz.tbi, called/N_1609.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-11.log jobid: 2484 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N2005.contig-group-10.g.vcf.gz, called/N2005.contig-group-10.g.vcf.gz.tbi, called/N2005.contig-group-10.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-10.log jobid: 2371 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-10.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1934_1_1_5973.contig-group-0.g.vcf.gz, called/N_1934_1_1_5973.contig-group-0.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-0.log jobid: 1370 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T185.contig-group-0.g.vcf.gz, called/T185.contig-group-0.g.vcf.gz.tbi, called/T185.contig-group-0.g.done log: logs/gatk/haplotypecaller/T185.contig-group-0.log jobid: 1472 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-0.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_6490.contig-group-3.g.vcf.gz, called/N_6490.contig-group-3.g.vcf.gz.tbi, called/N_6490.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-3.log jobid: 1746 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T196.contig-group-17.g.vcf.gz, called/T196.contig-group-17.g.vcf.gz.tbi, called/T196.contig-group-17.g.done log: logs/gatk/haplotypecaller/T196.contig-group-17.log jobid: 3127 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-17.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_9449.contig-group-23.g.vcf.gz, called/N_9449.contig-group-23.g.vcf.gz.tbi, called/N_9449.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-23.log jobid: 3686 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_9104.contig-group-10.g.vcf.gz, called/N_9104.contig-group-10.g.vcf.gz.tbi, called/N_9104.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-10.log jobid: 2437 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_8565.contig-group-18.g.vcf.gz, called/N_8565.contig-group-18.g.vcf.gz.tbi, called/N_8565.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-18.log jobid: 3201 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1927.contig-group-25.g.vcf.gz, called/N_1927.contig-group-25.g.vcf.gz.tbi, called/N_1927.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-25.log jobid: 3832 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1156.contig-group-12.g.vcf.gz, called/N_1156.contig-group-12.g.vcf.gz.tbi, called/N_1156.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-12.log jobid: 2566 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1157.contig-group-22.g.vcf.gz, called/N_1157.contig-group-22.g.vcf.gz.tbi, called/N_1157.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-22.log jobid: 3527 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_8171.contig-group-4.g.vcf.gz, called/N_8171.contig-group-4.g.vcf.gz.tbi, called/N_8171.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-4.log jobid: 1854 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_689.contig-group-13.g.vcf.gz, called/N_689.contig-group-13.g.vcf.gz.tbi, called/N_689.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-13.log jobid: 2708 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_9104.contig-group-3.g.vcf.gz, called/N_9104.contig-group-3.g.vcf.gz.tbi, called/N_9104.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-3.log jobid: 1765 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_2003_5409.contig-group-26.g.vcf.gz, called/N_2003_5409.contig-group-26.g.vcf.gz.tbi, called/N_2003_5409.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-26.log jobid: 3938 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_6928.contig-group-8.g.vcf.gz, called/N_6928.contig-group-8.g.vcf.gz.tbi, called/N_6928.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-8.log jobid: 2231 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_4843.contig-group-2.g.vcf.gz, called/N_4843.contig-group-2.g.vcf.gz.tbi, called/N_4843.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-2.log jobid: 1642 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1157.contig-group-16.g.vcf.gz, called/N_1157.contig-group-16.g.vcf.gz.tbi, called/N_1157.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-16.log jobid: 2951 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1870.contig-group-1.g.vcf.gz, called/N_1870.contig-group-1.g.vcf.gz.tbi, called/N_1870.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-1.log jobid: 1525 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_8565.contig-group-23.g.vcf.gz, called/N_8565.contig-group-23.g.vcf.gz.tbi, called/N_8565.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-23.log jobid: 3681 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_690.contig-group-21.g.vcf.gz, called/N_690.contig-group-21.g.vcf.gz.tbi, called/N_690.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-21.log jobid: 3477 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_6489.contig-group-15.g.vcf.gz, called/N_6489.contig-group-15.g.vcf.gz.tbi, called/N_6489.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-15.log jobid: 2897 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_690.contig-group-5.g.vcf.gz, called/N_690.contig-group-5.g.vcf.gz.tbi, called/N_690.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-5.log jobid: 1941 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_102.contig-group-0.g.vcf.gz, called/N_102.contig-group-0.g.vcf.gz.tbi, called/N_102.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-0.log jobid: 1324 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_102.contig-group-12.g.vcf.gz, called/N_102.contig-group-12.g.vcf.gz.tbi, called/N_102.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-12.log jobid: 2564 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/M5672.contig-group-3.g.vcf.gz, called/M5672.contig-group-3.g.vcf.gz.tbi, called/M5672.contig-group-3.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-3.log jobid: 1697 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-3.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1157.contig-group-20.g.vcf.gz, called/N_1157.contig-group-20.g.vcf.gz.tbi, called/N_1157.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-20.log jobid: 3335 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_4847.contig-group-1.g.vcf.gz, called/N_4847.contig-group-1.g.vcf.gz.tbi, called/N_4847.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-1.log jobid: 1549 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_2003_5409.contig-group-21.g.vcf.gz, called/N_2003_5409.contig-group-21.g.vcf.gz.tbi, called/N_2003_5409.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-21.log jobid: 3458 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_79.contig-group-17.g.vcf.gz, called/N_79.contig-group-17.g.vcf.gz.tbi, called/N_79.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-17.log jobid: 3099 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_4843.contig-group-6.g.vcf.gz, called/N_4843.contig-group-6.g.vcf.gz.tbi, called/N_4843.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-6.log jobid: 2026 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_8583.contig-group-21.g.vcf.gz, called/N_8583.contig-group-21.g.vcf.gz.tbi, called/N_8583.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-21.log jobid: 3490 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_8171.contig-group-2.g.vcf.gz, called/N_8171.contig-group-2.g.vcf.gz.tbi, called/N_8171.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-2.log jobid: 1662 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_351.contig-group-11.g.vcf.gz, called/N_351.contig-group-11.g.vcf.gz.tbi, called/N_351.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-11.log jobid: 2502 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_6490.contig-group-2.g.vcf.gz, called/N_6490.contig-group-2.g.vcf.gz.tbi, called/N_6490.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-2.log jobid: 1650 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_9449.contig-group-9.g.vcf.gz, called/N_9449.contig-group-9.g.vcf.gz.tbi, called/N_9449.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-9.log jobid: 2342 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_6928.contig-group-19.g.vcf.gz, called/N_6928.contig-group-19.g.vcf.gz.tbi, called/N_6928.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-19.log jobid: 3287 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1158.contig-group-1.g.vcf.gz, called/N_1158.contig-group-1.g.vcf.gz.tbi, called/N_1158.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-1.log jobid: 1512 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_8171.contig-group-9.g.vcf.gz, called/N_8171.contig-group-9.g.vcf.gz.tbi, called/N_8171.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-9.log jobid: 2334 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_6490.contig-group-7.g.vcf.gz, called/N_6490.contig-group-7.g.vcf.gz.tbi, called/N_6490.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-7.log jobid: 2130 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T187.contig-group-4.g.vcf.gz, called/T187.contig-group-4.g.vcf.gz.tbi, called/T187.contig-group-4.g.done log: logs/gatk/haplotypecaller/T187.contig-group-4.log jobid: 1872 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-4.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1157.contig-group-1.g.vcf.gz, called/N_1157.contig-group-1.g.vcf.gz.tbi, called/N_1157.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-1.log jobid: 1511 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1386.contig-group-21.g.vcf.gz, called/N_1386.contig-group-21.g.vcf.gz.tbi, called/N_1386.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-21.log jobid: 3438 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_2003_5409.contig-group-20.g.vcf.gz, called/N_2003_5409.contig-group-20.g.vcf.gz.tbi, called/N_2003_5409.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-20.log jobid: 3362 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_351.contig-group-13.g.vcf.gz, called/N_351.contig-group-13.g.vcf.gz.tbi, called/N_351.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-13.log jobid: 2694 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T187.contig-group-10.g.vcf.gz, called/T187.contig-group-10.g.vcf.gz.tbi, called/T187.contig-group-10.g.done log: logs/gatk/haplotypecaller/T187.contig-group-10.log jobid: 2448 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-10.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1157.contig-group-11.g.vcf.gz, called/N_1157.contig-group-11.g.vcf.gz.tbi, called/N_1157.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-11.log jobid: 2471 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/M5672.contig-group-19.g.vcf.gz, called/M5672.contig-group-19.g.vcf.gz.tbi, called/M5672.contig-group-19.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-19.log jobid: 3233 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-19.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T79.contig-group-26.g.vcf.gz, called/T79.contig-group-26.g.vcf.gz.tbi, called/T79.contig-group-26.g.done log: logs/gatk/haplotypecaller/T79.contig-group-26.log jobid: 3995 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-26.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_9449.contig-group-2.g.vcf.gz, called/N_9449.contig-group-2.g.vcf.gz.tbi, called/N_9449.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-2.log jobid: 1670 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_5129.contig-group-8.g.vcf.gz, called/N_5129.contig-group-8.g.vcf.gz.tbi, called/N_5129.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-8.log jobid: 2224 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T190.contig-group-8.g.vcf.gz, called/T190.contig-group-8.g.vcf.gz.tbi, called/T190.contig-group-8.g.done log: logs/gatk/haplotypecaller/T190.contig-group-8.log jobid: 2259 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-8.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_102.contig-group-25.g.vcf.gz, called/N_102.contig-group-25.g.vcf.gz.tbi, called/N_102.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-25.log jobid: 3812 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_689.contig-group-9.g.vcf.gz, called/N_689.contig-group-9.g.vcf.gz.tbi, called/N_689.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-9.log jobid: 2324 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T180.contig-group-24.g.vcf.gz, called/T180.contig-group-24.g.vcf.gz.tbi, called/T180.contig-group-24.g.done log: logs/gatk/haplotypecaller/T180.contig-group-24.log jobid: 3788 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-24.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1609.contig-group-20.g.vcf.gz, called/N_1609.contig-group-20.g.vcf.gz.tbi, called/N_1609.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-20.log jobid: 3348 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T187.contig-group-22.g.vcf.gz, called/T187.contig-group-22.g.vcf.gz.tbi, called/T187.contig-group-22.g.done log: logs/gatk/haplotypecaller/T187.contig-group-22.log jobid: 3600 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-22.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_102.contig-group-14.g.vcf.gz, called/N_102.contig-group-14.g.vcf.gz.tbi, called/N_102.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-14.log jobid: 2756 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1609.contig-group-1.g.vcf.gz, called/N_1609.contig-group-1.g.vcf.gz.tbi, called/N_1609.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-1.log jobid: 1524 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_6928.contig-group-16.g.vcf.gz, called/N_6928.contig-group-16.g.vcf.gz.tbi, called/N_6928.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-16.log jobid: 2999 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_9104.contig-group-21.g.vcf.gz, called/N_9104.contig-group-21.g.vcf.gz.tbi, called/N_9104.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-21.log jobid: 3493 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_83.contig-group-13.g.vcf.gz, called/N_83.contig-group-13.g.vcf.gz.tbi, called/N_83.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-13.log jobid: 2719 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_6489.contig-group-2.g.vcf.gz, called/N_6489.contig-group-2.g.vcf.gz.tbi, called/N_6489.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-2.log jobid: 1649 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T1483.contig-group-8.g.vcf.gz, called/T1483.contig-group-8.g.vcf.gz.tbi, called/T1483.contig-group-8.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-8.log jobid: 2249 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-8.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_4847.contig-group-12.g.vcf.gz, called/N_4847.contig-group-12.g.vcf.gz.tbi, called/N_4847.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-12.log jobid: 2605 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T192.contig-group-2.g.vcf.gz, called/T192.contig-group-2.g.vcf.gz.tbi, called/T192.contig-group-2.g.done log: logs/gatk/haplotypecaller/T192.contig-group-2.log jobid: 1684 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-2.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_102.contig-group-24.g.vcf.gz, called/N_102.contig-group-24.g.vcf.gz.tbi, called/N_102.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-24.log jobid: 3716 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1992_0123.contig-group-20.g.vcf.gz, called/N_1992_0123.contig-group-20.g.vcf.gz.tbi, called/N_1992_0123.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-20.log jobid: 3357 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1870.contig-group-18.g.vcf.gz, called/N_1870.contig-group-18.g.vcf.gz.tbi, called/N_1870.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-18.log jobid: 3157 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N2005.contig-group-24.g.vcf.gz, called/N2005.contig-group-24.g.vcf.gz.tbi, called/N2005.contig-group-24.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-24.log jobid: 3715 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-24.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1609.contig-group-24.g.vcf.gz, called/N_1609.contig-group-24.g.vcf.gz.tbi, called/N_1609.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-24.log jobid: 3732 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T72.contig-group-12.g.vcf.gz, called/T72.contig-group-12.g.vcf.gz.tbi, called/T72.contig-group-12.g.done log: logs/gatk/haplotypecaller/T72.contig-group-12.log jobid: 2650 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-12.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_83.contig-group-5.g.vcf.gz, called/N_83.contig-group-5.g.vcf.gz.tbi, called/N_83.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-5.log jobid: 1951 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_6490.contig-group-6.g.vcf.gz, called/N_6490.contig-group-6.g.vcf.gz.tbi, called/N_6490.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-6.log jobid: 2034 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T196.contig-group-18.g.vcf.gz, called/T196.contig-group-18.g.vcf.gz.tbi, called/T196.contig-group-18.g.done log: logs/gatk/haplotypecaller/T196.contig-group-18.log jobid: 3223 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-18.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_2003_5409.contig-group-14.g.vcf.gz, called/N_2003_5409.contig-group-14.g.vcf.gz.tbi, called/N_2003_5409.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-14.log jobid: 2786 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T1483.contig-group-9.g.vcf.gz, called/T1483.contig-group-9.g.vcf.gz.tbi, called/T1483.contig-group-9.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-9.log jobid: 2345 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-9.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_9104.contig-group-6.g.vcf.gz, called/N_9104.contig-group-6.g.vcf.gz.tbi, called/N_9104.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-6.log jobid: 2053 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_9449.contig-group-24.g.vcf.gz, called/N_9449.contig-group-24.g.vcf.gz.tbi, called/N_9449.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-24.log jobid: 3782 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_2003_5409.contig-group-25.g.vcf.gz, called/N_2003_5409.contig-group-25.g.vcf.gz.tbi, called/N_2003_5409.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-25.log jobid: 3842 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N2005.contig-group-25.g.vcf.gz, called/N2005.contig-group-25.g.vcf.gz.tbi, called/N2005.contig-group-25.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-25.log jobid: 3811 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-25.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_9104.contig-group-2.g.vcf.gz, called/N_9104.contig-group-2.g.vcf.gz.tbi, called/N_9104.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-2.log jobid: 1669 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T192.contig-group-11.g.vcf.gz, called/T192.contig-group-11.g.vcf.gz.tbi, called/T192.contig-group-11.g.done log: logs/gatk/haplotypecaller/T192.contig-group-11.log jobid: 2548 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-11.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_9449.contig-group-3.g.vcf.gz, called/N_9449.contig-group-3.g.vcf.gz.tbi, called/N_9449.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-3.log jobid: 1766 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_6490.contig-group-14.g.vcf.gz, called/N_6490.contig-group-14.g.vcf.gz.tbi, called/N_6490.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-14.log jobid: 2802 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_690.contig-group-11.g.vcf.gz, called/N_690.contig-group-11.g.vcf.gz.tbi, called/N_690.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-11.log jobid: 2517 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/M5672.contig-group-20.g.vcf.gz, called/M5672.contig-group-20.g.vcf.gz.tbi, called/M5672.contig-group-20.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-20.log jobid: 3329 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-20.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_79.contig-group-5.g.vcf.gz, called/N_79.contig-group-5.g.vcf.gz.tbi, called/N_79.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-5.log jobid: 1947 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_690.contig-group-23.g.vcf.gz, called/N_690.contig-group-23.g.vcf.gz.tbi, called/N_690.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-23.log jobid: 3669 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_690.contig-group-24.g.vcf.gz, called/N_690.contig-group-24.g.vcf.gz.tbi, called/N_690.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-24.log jobid: 3765 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T180.contig-group-16.g.vcf.gz, called/T180.contig-group-16.g.vcf.gz.tbi, called/T180.contig-group-16.g.done log: logs/gatk/haplotypecaller/T180.contig-group-16.log jobid: 3020 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-16.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_4843.contig-group-8.g.vcf.gz, called/N_4843.contig-group-8.g.vcf.gz.tbi, called/N_4843.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-8.log jobid: 2218 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_5129.contig-group-14.g.vcf.gz, called/N_5129.contig-group-14.g.vcf.gz.tbi, called/N_5129.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-14.log jobid: 2800 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1386.contig-group-16.g.vcf.gz, called/N_1386.contig-group-16.g.vcf.gz.tbi, called/N_1386.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-16.log jobid: 2958 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1870.contig-group-25.g.vcf.gz, called/N_1870.contig-group-25.g.vcf.gz.tbi, called/N_1870.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-25.log jobid: 3829 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T72.contig-group-16.g.vcf.gz, called/T72.contig-group-16.g.vcf.gz.tbi, called/T72.contig-group-16.g.done log: logs/gatk/haplotypecaller/T72.contig-group-16.log jobid: 3034 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-16.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1927.contig-group-14.g.vcf.gz, called/N_1927.contig-group-14.g.vcf.gz.tbi, called/N_1927.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-14.log jobid: 2776 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1870.contig-group-22.g.vcf.gz, called/N_1870.contig-group-22.g.vcf.gz.tbi, called/N_1870.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-22.log jobid: 3541 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_2003_5409.contig-group-16.g.vcf.gz, called/N_2003_5409.contig-group-16.g.vcf.gz.tbi, called/N_2003_5409.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-16.log jobid: 2978 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_6490.contig-group-13.g.vcf.gz, called/N_6490.contig-group-13.g.vcf.gz.tbi, called/N_6490.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-13.log jobid: 2706 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_8583.contig-group-14.g.vcf.gz, called/N_8583.contig-group-14.g.vcf.gz.tbi, called/N_8583.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-14.log jobid: 2818 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T196.contig-group-25.g.vcf.gz, called/T196.contig-group-25.g.vcf.gz.tbi, called/T196.contig-group-25.g.done log: logs/gatk/haplotypecaller/T196.contig-group-25.log jobid: 3895 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-25.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_2003_5409.contig-group-8.g.vcf.gz, called/N_2003_5409.contig-group-8.g.vcf.gz.tbi, called/N_2003_5409.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-8.log jobid: 2210 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T185.contig-group-8.g.vcf.gz, called/T185.contig-group-8.g.vcf.gz.tbi, called/T185.contig-group-8.g.done log: logs/gatk/haplotypecaller/T185.contig-group-8.log jobid: 2254 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-8.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T185.contig-group-18.g.vcf.gz, called/T185.contig-group-18.g.vcf.gz.tbi, called/T185.contig-group-18.g.done log: logs/gatk/haplotypecaller/T185.contig-group-18.log jobid: 3214 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-18.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_102.contig-group-7.g.vcf.gz, called/N_102.contig-group-7.g.vcf.gz.tbi, called/N_102.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-7.log jobid: 2084 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_690.contig-group-0.g.vcf.gz, called/N_690.contig-group-0.g.vcf.gz.tbi, called/N_690.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-0.log jobid: 1422 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-0.bench.log reason: Missing output files: called/N_690.contig-group-0.g.vcf.gz, called/N_690.contig-group-0.g.vcf.gz.tbi; Updated input files: dedup/N_690.bam, contig-groups/contig-group-0.bed; Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_8583.contig-group-17.g.vcf.gz, called/N_8583.contig-group-17.g.vcf.gz.tbi, called/N_8583.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-17.log jobid: 3106 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T180.contig-group-25.g.vcf.gz, called/T180.contig-group-25.g.vcf.gz.tbi, called/T180.contig-group-25.g.done log: logs/gatk/haplotypecaller/T180.contig-group-25.log jobid: 3884 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-25.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T185.contig-group-10.g.vcf.gz, called/T185.contig-group-10.g.vcf.gz.tbi, called/T185.contig-group-10.g.done log: logs/gatk/haplotypecaller/T185.contig-group-10.log jobid: 2446 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-10.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T72.contig-group-26.g.vcf.gz, called/T72.contig-group-26.g.vcf.gz.tbi, called/T72.contig-group-26.g.done log: logs/gatk/haplotypecaller/T72.contig-group-26.log jobid: 3994 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-26.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1927.contig-group-18.g.vcf.gz, called/N_1927.contig-group-18.g.vcf.gz.tbi, called/N_1927.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-18.log jobid: 3160 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_351.contig-group-15.g.vcf.gz, called/N_351.contig-group-15.g.vcf.gz.tbi, called/N_351.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-15.log jobid: 2886 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T187.contig-group-18.g.vcf.gz, called/T187.contig-group-18.g.vcf.gz.tbi, called/T187.contig-group-18.g.done log: logs/gatk/haplotypecaller/T187.contig-group-18.log jobid: 3216 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-18.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_9104.contig-group-0.g.vcf.gz, called/N_9104.contig-group-0.g.vcf.gz.tbi, called/N_9104.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-0.log jobid: 1454 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T196.contig-group-12.g.vcf.gz, called/T196.contig-group-12.g.vcf.gz.tbi, called/T196.contig-group-12.g.done log: logs/gatk/haplotypecaller/T196.contig-group-12.log jobid: 2647 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-12.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_8583.contig-group-3.g.vcf.gz, called/N_8583.contig-group-3.g.vcf.gz.tbi, called/N_8583.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-3.log jobid: 1762 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_79.contig-group-18.g.vcf.gz, called/N_79.contig-group-18.g.vcf.gz.tbi, called/N_79.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-18.log jobid: 3195 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T185.contig-group-4.g.vcf.gz, called/T185.contig-group-4.g.vcf.gz.tbi, called/T185.contig-group-4.g.done log: logs/gatk/haplotypecaller/T185.contig-group-4.log jobid: 1870 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-4.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_2003_5409.contig-group-7.g.vcf.gz, called/N_2003_5409.contig-group-7.g.vcf.gz.tbi, called/N_2003_5409.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-7.log jobid: 2114 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T187.contig-group-23.g.vcf.gz, called/T187.contig-group-23.g.vcf.gz.tbi, called/T187.contig-group-23.g.done log: logs/gatk/haplotypecaller/T187.contig-group-23.log jobid: 3696 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-23.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_4843.contig-group-24.g.vcf.gz, called/N_4843.contig-group-24.g.vcf.gz.tbi, called/N_4843.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-24.log jobid: 3754 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_6490.contig-group-9.g.vcf.gz, called/N_6490.contig-group-9.g.vcf.gz.tbi, called/N_6490.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-9.log jobid: 2322 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_8583.contig-group-23.g.vcf.gz, called/N_8583.contig-group-23.g.vcf.gz.tbi, called/N_8583.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-23.log jobid: 3682 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_8565.contig-group-7.g.vcf.gz, called/N_8565.contig-group-7.g.vcf.gz.tbi, called/N_8565.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-7.log jobid: 2145 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_6928.contig-group-24.g.vcf.gz, called/N_6928.contig-group-24.g.vcf.gz.tbi, called/N_6928.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-24.log jobid: 3767 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1354.contig-group-25.g.vcf.gz, called/N_1354.contig-group-25.g.vcf.gz.tbi, called/N_1354.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-25.log jobid: 3819 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_351.contig-group-3.g.vcf.gz, called/N_351.contig-group-3.g.vcf.gz.tbi, called/N_351.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-3.log jobid: 1734 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N2005.contig-group-17.g.vcf.gz, called/N2005.contig-group-17.g.vcf.gz.tbi, called/N2005.contig-group-17.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-17.log jobid: 3043 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-17.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T185.contig-group-5.g.vcf.gz, called/T185.contig-group-5.g.vcf.gz.tbi, called/T185.contig-group-5.g.done log: logs/gatk/haplotypecaller/T185.contig-group-5.log jobid: 1966 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-5.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_8171.contig-group-21.g.vcf.gz, called/N_8171.contig-group-21.g.vcf.gz.tbi, called/N_8171.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-21.log jobid: 3486 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_4847.contig-group-2.g.vcf.gz, called/N_4847.contig-group-2.g.vcf.gz.tbi, called/N_4847.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-2.log jobid: 1645 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_4847.contig-group-19.g.vcf.gz, called/N_4847.contig-group-19.g.vcf.gz.tbi, called/N_4847.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-19.log jobid: 3277 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_6489.contig-group-4.g.vcf.gz, called/N_6489.contig-group-4.g.vcf.gz.tbi, called/N_6489.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-4.log jobid: 1841 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1870.contig-group-9.g.vcf.gz, called/N_1870.contig-group-9.g.vcf.gz.tbi, called/N_1870.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-9.log jobid: 2293 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1609.contig-group-17.g.vcf.gz, called/N_1609.contig-group-17.g.vcf.gz.tbi, called/N_1609.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-17.log jobid: 3060 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T196.contig-group-16.g.vcf.gz, called/T196.contig-group-16.g.vcf.gz.tbi, called/T196.contig-group-16.g.done log: logs/gatk/haplotypecaller/T196.contig-group-16.log jobid: 3031 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-16.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_8583.contig-group-1.g.vcf.gz, called/N_8583.contig-group-1.g.vcf.gz.tbi, called/N_8583.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-1.log jobid: 1570 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N2005.contig-group-6.g.vcf.gz, called/N2005.contig-group-6.g.vcf.gz.tbi, called/N2005.contig-group-6.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-6.log jobid: 1987 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-6.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_4847.contig-group-8.g.vcf.gz, called/N_4847.contig-group-8.g.vcf.gz.tbi, called/N_4847.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-8.log jobid: 2221 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_83.contig-group-8.g.vcf.gz, called/N_83.contig-group-8.g.vcf.gz.tbi, called/N_83.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-8.log jobid: 2239 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1927.contig-group-1.g.vcf.gz, called/N_1927.contig-group-1.g.vcf.gz.tbi, called/N_1927.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-1.log jobid: 1528 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_4843.contig-group-14.g.vcf.gz, called/N_4843.contig-group-14.g.vcf.gz.tbi, called/N_4843.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-14.log jobid: 2794 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1386.contig-group-9.g.vcf.gz, called/N_1386.contig-group-9.g.vcf.gz.tbi, called/N_1386.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-9.log jobid: 2286 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/M5672.contig-group-21.g.vcf.gz, called/M5672.contig-group-21.g.vcf.gz.tbi, called/M5672.contig-group-21.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-21.log jobid: 3425 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-21.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_6490.contig-group-4.g.vcf.gz, called/N_6490.contig-group-4.g.vcf.gz.tbi, called/N_6490.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-4.log jobid: 1842 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1992_0123.contig-group-2.g.vcf.gz, called/N_1992_0123.contig-group-2.g.vcf.gz.tbi, called/N_1992_0123.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-2.log jobid: 1629 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_6489.contig-group-8.g.vcf.gz, called/N_6489.contig-group-8.g.vcf.gz.tbi, called/N_6489.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-8.log jobid: 2225 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_5129.contig-group-7.g.vcf.gz, called/N_5129.contig-group-7.g.vcf.gz.tbi, called/N_5129.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-7.log jobid: 2128 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_4847.contig-group-24.g.vcf.gz, called/N_4847.contig-group-24.g.vcf.gz.tbi, called/N_4847.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-24.log jobid: 3757 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_79.contig-group-10.g.vcf.gz, called/N_79.contig-group-10.g.vcf.gz.tbi, called/N_79.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-10.log jobid: 2427 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_79.contig-group-26.g.vcf.gz, called/N_79.contig-group-26.g.vcf.gz.tbi, called/N_79.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-26.log jobid: 3963 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T190.contig-group-2.g.vcf.gz, called/T190.contig-group-2.g.vcf.gz.tbi, called/T190.contig-group-2.g.done log: logs/gatk/haplotypecaller/T190.contig-group-2.log jobid: 1683 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-2.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/M5672.contig-group-12.g.vcf.gz, called/M5672.contig-group-12.g.vcf.gz.tbi, called/M5672.contig-group-12.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-12.log jobid: 2561 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-12.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_6928.contig-group-14.g.vcf.gz, called/N_6928.contig-group-14.g.vcf.gz.tbi, called/N_6928.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-14.log jobid: 2807 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_8565.contig-group-15.g.vcf.gz, called/N_8565.contig-group-15.g.vcf.gz.tbi, called/N_8565.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-15.log jobid: 2913 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/M5672.contig-group-4.g.vcf.gz, called/M5672.contig-group-4.g.vcf.gz.tbi, called/M5672.contig-group-4.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-4.log jobid: 1793 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-4.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_9449.contig-group-4.g.vcf.gz, called/N_9449.contig-group-4.g.vcf.gz.tbi, called/N_9449.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-4.log jobid: 1862 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_8171.contig-group-26.g.vcf.gz, called/N_8171.contig-group-26.g.vcf.gz.tbi, called/N_8171.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-26.log jobid: 3966 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_5129.contig-group-6.g.vcf.gz, called/N_5129.contig-group-6.g.vcf.gz.tbi, called/N_5129.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-6.log jobid: 2032 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T72.contig-group-23.g.vcf.gz, called/T72.contig-group-23.g.vcf.gz.tbi, called/T72.contig-group-23.g.done log: logs/gatk/haplotypecaller/T72.contig-group-23.log jobid: 3706 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-23.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1934_1_1_5973.contig-group-15.g.vcf.gz, called/N_1934_1_1_5973.contig-group-15.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-15.log jobid: 2875 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1609.contig-group-19.g.vcf.gz, called/N_1609.contig-group-19.g.vcf.gz.tbi, called/N_1609.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-19.log jobid: 3252 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_6928.contig-group-11.g.vcf.gz, called/N_6928.contig-group-11.g.vcf.gz.tbi, called/N_6928.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-11.log jobid: 2519 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_102.contig-group-21.g.vcf.gz, called/N_102.contig-group-21.g.vcf.gz.tbi, called/N_102.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-21.log jobid: 3428 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_9449.contig-group-25.g.vcf.gz, called/N_9449.contig-group-25.g.vcf.gz.tbi, called/N_9449.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-25.log jobid: 3878 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T190.contig-group-5.g.vcf.gz, called/T190.contig-group-5.g.vcf.gz.tbi, called/T190.contig-group-5.g.done log: logs/gatk/haplotypecaller/T190.contig-group-5.log jobid: 1971 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-5.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_5129.contig-group-16.g.vcf.gz, called/N_5129.contig-group-16.g.vcf.gz.tbi, called/N_5129.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-16.log jobid: 2992 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_4843.contig-group-4.g.vcf.gz, called/N_4843.contig-group-4.g.vcf.gz.tbi, called/N_4843.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-4.log jobid: 1834 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_79.contig-group-22.g.vcf.gz, called/N_79.contig-group-22.g.vcf.gz.tbi, called/N_79.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-22.log jobid: 3579 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_8565.contig-group-19.g.vcf.gz, called/N_8565.contig-group-19.g.vcf.gz.tbi, called/N_8565.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-19.log jobid: 3297 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_351.contig-group-22.g.vcf.gz, called/N_351.contig-group-22.g.vcf.gz.tbi, called/N_351.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-22.log jobid: 3558 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T72.contig-group-15.g.vcf.gz, called/T72.contig-group-15.g.vcf.gz.tbi, called/T72.contig-group-15.g.done log: logs/gatk/haplotypecaller/T72.contig-group-15.log jobid: 2938 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-15.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_6489.contig-group-12.g.vcf.gz, called/N_6489.contig-group-12.g.vcf.gz.tbi, called/N_6489.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-12.log jobid: 2609 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_102.contig-group-18.g.vcf.gz, called/N_102.contig-group-18.g.vcf.gz.tbi, called/N_102.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-18.log jobid: 3140 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1157.contig-group-13.g.vcf.gz, called/N_1157.contig-group-13.g.vcf.gz.tbi, called/N_1157.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-13.log jobid: 2663 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_79.contig-group-12.g.vcf.gz, called/N_79.contig-group-12.g.vcf.gz.tbi, called/N_79.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-12.log jobid: 2619 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1354.contig-group-23.g.vcf.gz, called/N_1354.contig-group-23.g.vcf.gz.tbi, called/N_1354.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-23.log jobid: 3627 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1870.contig-group-15.g.vcf.gz, called/N_1870.contig-group-15.g.vcf.gz.tbi, called/N_1870.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-15.log jobid: 2869 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T190.contig-group-7.g.vcf.gz, called/T190.contig-group-7.g.vcf.gz.tbi, called/T190.contig-group-7.g.done log: logs/gatk/haplotypecaller/T190.contig-group-7.log jobid: 2163 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-7.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1870.contig-group-4.g.vcf.gz, called/N_1870.contig-group-4.g.vcf.gz.tbi, called/N_1870.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-4.log jobid: 1813 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_6928.contig-group-2.g.vcf.gz, called/N_6928.contig-group-2.g.vcf.gz.tbi, called/N_6928.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-2.log jobid: 1655 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1156.contig-group-10.g.vcf.gz, called/N_1156.contig-group-10.g.vcf.gz.tbi, called/N_1156.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-10.log jobid: 2374 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_689.contig-group-5.g.vcf.gz, called/N_689.contig-group-5.g.vcf.gz.tbi, called/N_689.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-5.log jobid: 1940 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_6489.contig-group-23.g.vcf.gz, called/N_6489.contig-group-23.g.vcf.gz.tbi, called/N_6489.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-23.log jobid: 3665 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_6489.contig-group-21.g.vcf.gz, called/N_6489.contig-group-21.g.vcf.gz.tbi, called/N_6489.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-21.log jobid: 3473 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_9104.contig-group-15.g.vcf.gz, called/N_9104.contig-group-15.g.vcf.gz.tbi, called/N_9104.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-15.log jobid: 2917 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_6489.contig-group-5.g.vcf.gz, called/N_6489.contig-group-5.g.vcf.gz.tbi, called/N_6489.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-5.log jobid: 1937 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T72.contig-group-7.g.vcf.gz, called/T72.contig-group-7.g.vcf.gz.tbi, called/T72.contig-group-7.g.done log: logs/gatk/haplotypecaller/T72.contig-group-7.log jobid: 2170 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-7.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1354.contig-group-18.g.vcf.gz, called/N_1354.contig-group-18.g.vcf.gz.tbi, called/N_1354.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-18.log jobid: 3147 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/M5672.contig-group-17.g.vcf.gz, called/M5672.contig-group-17.g.vcf.gz.tbi, called/M5672.contig-group-17.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-17.log jobid: 3041 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-17.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_8565.contig-group-26.g.vcf.gz, called/N_8565.contig-group-26.g.vcf.gz.tbi, called/N_8565.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-26.log jobid: 3969 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1354.contig-group-0.g.vcf.gz, called/N_1354.contig-group-0.g.vcf.gz.tbi, called/N_1354.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-0.log jobid: 1338 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T185.contig-group-6.g.vcf.gz, called/T185.contig-group-6.g.vcf.gz.tbi, called/T185.contig-group-6.g.done log: logs/gatk/haplotypecaller/T185.contig-group-6.log jobid: 2062 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-6.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_351.contig-group-10.g.vcf.gz, called/N_351.contig-group-10.g.vcf.gz.tbi, called/N_351.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-10.log jobid: 2406 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_6928.contig-group-15.g.vcf.gz, called/N_6928.contig-group-15.g.vcf.gz.tbi, called/N_6928.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-15.log jobid: 2903 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_4843.contig-group-13.g.vcf.gz, called/N_4843.contig-group-13.g.vcf.gz.tbi, called/N_4843.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-13.log jobid: 2698 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1158.contig-group-2.g.vcf.gz, called/N_1158.contig-group-2.g.vcf.gz.tbi, called/N_1158.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-2.log jobid: 1608 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1156.contig-group-23.g.vcf.gz, called/N_1156.contig-group-23.g.vcf.gz.tbi, called/N_1156.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-23.log jobid: 3622 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_8565.contig-group-11.g.vcf.gz, called/N_8565.contig-group-11.g.vcf.gz.tbi, called/N_8565.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-11.log jobid: 2529 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1992_0123.contig-group-5.g.vcf.gz, called/N_1992_0123.contig-group-5.g.vcf.gz.tbi, called/N_1992_0123.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-5.log jobid: 1917 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_2003_5409.contig-group-12.g.vcf.gz, called/N_2003_5409.contig-group-12.g.vcf.gz.tbi, called/N_2003_5409.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-12.log jobid: 2594 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T190.contig-group-6.g.vcf.gz, called/T190.contig-group-6.g.vcf.gz.tbi, called/T190.contig-group-6.g.done log: logs/gatk/haplotypecaller/T190.contig-group-6.log jobid: 2067 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-6.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1354.contig-group-21.g.vcf.gz, called/N_1354.contig-group-21.g.vcf.gz.tbi, called/N_1354.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-21.log jobid: 3435 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1156.contig-group-15.g.vcf.gz, called/N_1156.contig-group-15.g.vcf.gz.tbi, called/N_1156.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-15.log jobid: 2854 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_8583.contig-group-9.g.vcf.gz, called/N_8583.contig-group-9.g.vcf.gz.tbi, called/N_8583.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-9.log jobid: 2338 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_9449.contig-group-18.g.vcf.gz, called/N_9449.contig-group-18.g.vcf.gz.tbi, called/N_9449.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-18.log jobid: 3206 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_8171.contig-group-12.g.vcf.gz, called/N_8171.contig-group-12.g.vcf.gz.tbi, called/N_8171.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-12.log jobid: 2622 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_83.contig-group-22.g.vcf.gz, called/N_83.contig-group-22.g.vcf.gz.tbi, called/N_83.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-22.log jobid: 3583 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_9449.contig-group-22.g.vcf.gz, called/N_9449.contig-group-22.g.vcf.gz.tbi, called/N_9449.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-22.log jobid: 3590 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_4843.contig-group-20.g.vcf.gz, called/N_4843.contig-group-20.g.vcf.gz.tbi, called/N_4843.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-20.log jobid: 3370 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_351.contig-group-2.g.vcf.gz, called/N_351.contig-group-2.g.vcf.gz.tbi, called/N_351.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-2.log jobid: 1638 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N2005.contig-group-7.g.vcf.gz, called/N2005.contig-group-7.g.vcf.gz.tbi, called/N2005.contig-group-7.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-7.log jobid: 2083 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-7.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T72.contig-group-8.g.vcf.gz, called/T72.contig-group-8.g.vcf.gz.tbi, called/T72.contig-group-8.g.done log: logs/gatk/haplotypecaller/T72.contig-group-8.log jobid: 2266 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-8.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_689.contig-group-1.g.vcf.gz, called/N_689.contig-group-1.g.vcf.gz.tbi, called/N_689.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-1.log jobid: 1556 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1934_1_1_5973.contig-group-25.g.vcf.gz, called/N_1934_1_1_5973.contig-group-25.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-25.log jobid: 3835 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_6928.contig-group-1.g.vcf.gz, called/N_6928.contig-group-1.g.vcf.gz.tbi, called/N_6928.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-1.log jobid: 1559 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1609.contig-group-4.g.vcf.gz, called/N_1609.contig-group-4.g.vcf.gz.tbi, called/N_1609.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-4.log jobid: 1812 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_102.contig-group-9.g.vcf.gz, called/N_102.contig-group-9.g.vcf.gz.tbi, called/N_102.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-9.log jobid: 2276 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T180.contig-group-15.g.vcf.gz, called/T180.contig-group-15.g.vcf.gz.tbi, called/T180.contig-group-15.g.done log: logs/gatk/haplotypecaller/T180.contig-group-15.log jobid: 2924 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-15.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T192.contig-group-4.g.vcf.gz, called/T192.contig-group-4.g.vcf.gz.tbi, called/T192.contig-group-4.g.done log: logs/gatk/haplotypecaller/T192.contig-group-4.log jobid: 1876 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-4.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_9104.contig-group-9.g.vcf.gz, called/N_9104.contig-group-9.g.vcf.gz.tbi, called/N_9104.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-9.log jobid: 2341 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1992_0123.contig-group-24.g.vcf.gz, called/N_1992_0123.contig-group-24.g.vcf.gz.tbi, called/N_1992_0123.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-24.log jobid: 3741 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T185.contig-group-20.g.vcf.gz, called/T185.contig-group-20.g.vcf.gz.tbi, called/T185.contig-group-20.g.done log: logs/gatk/haplotypecaller/T185.contig-group-20.log jobid: 3406 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-20.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_9104.contig-group-26.g.vcf.gz, called/N_9104.contig-group-26.g.vcf.gz.tbi, called/N_9104.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-26.log jobid: 3973 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_6928.contig-group-13.g.vcf.gz, called/N_6928.contig-group-13.g.vcf.gz.tbi, called/N_6928.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-13.log jobid: 2711 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1870.contig-group-14.g.vcf.gz, called/N_1870.contig-group-14.g.vcf.gz.tbi, called/N_1870.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-14.log jobid: 2773 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T187.contig-group-7.g.vcf.gz, called/T187.contig-group-7.g.vcf.gz.tbi, called/T187.contig-group-7.g.done log: logs/gatk/haplotypecaller/T187.contig-group-7.log jobid: 2160 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-7.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/M5672.contig-group-15.g.vcf.gz, called/M5672.contig-group-15.g.vcf.gz.tbi, called/M5672.contig-group-15.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-15.log jobid: 2849 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-15.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T192.contig-group-6.g.vcf.gz, called/T192.contig-group-6.g.vcf.gz.tbi, called/T192.contig-group-6.g.done log: logs/gatk/haplotypecaller/T192.contig-group-6.log jobid: 2068 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-6.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_6490.contig-group-8.g.vcf.gz, called/N_6490.contig-group-8.g.vcf.gz.tbi, called/N_6490.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-8.log jobid: 2226 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1934_1_1_5973.contig-group-3.g.vcf.gz, called/N_1934_1_1_5973.contig-group-3.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-3.log jobid: 1723 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_79.contig-group-23.g.vcf.gz, called/N_79.contig-group-23.g.vcf.gz.tbi, called/N_79.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-23.log jobid: 3675 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_2003_5409.contig-group-17.g.vcf.gz, called/N_2003_5409.contig-group-17.g.vcf.gz.tbi, called/N_2003_5409.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-17.log jobid: 3074 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1934_1_1_5973.contig-group-18.g.vcf.gz, called/N_1934_1_1_5973.contig-group-18.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-18.log jobid: 3163 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T187.contig-group-6.g.vcf.gz, called/T187.contig-group-6.g.vcf.gz.tbi, called/T187.contig-group-6.g.done log: logs/gatk/haplotypecaller/T187.contig-group-6.log jobid: 2064 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-6.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_79.contig-group-19.g.vcf.gz, called/N_79.contig-group-19.g.vcf.gz.tbi, called/N_79.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-19.log jobid: 3291 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_6490.contig-group-18.g.vcf.gz, called/N_6490.contig-group-18.g.vcf.gz.tbi, called/N_6490.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-18.log jobid: 3186 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1157.contig-group-21.g.vcf.gz, called/N_1157.contig-group-21.g.vcf.gz.tbi, called/N_1157.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-21.log jobid: 3431 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T1483.contig-group-14.g.vcf.gz, called/T1483.contig-group-14.g.vcf.gz.tbi, called/T1483.contig-group-14.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-14.log jobid: 2825 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-14.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_2003_5409.contig-group-5.g.vcf.gz, called/N_2003_5409.contig-group-5.g.vcf.gz.tbi, called/N_2003_5409.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-5.log jobid: 1922 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/M5672.contig-group-24.g.vcf.gz, called/M5672.contig-group-24.g.vcf.gz.tbi, called/M5672.contig-group-24.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-24.log jobid: 3713 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-24.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_689.contig-group-15.g.vcf.gz, called/N_689.contig-group-15.g.vcf.gz.tbi, called/N_689.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-15.log jobid: 2900 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T79.contig-group-3.g.vcf.gz, called/T79.contig-group-3.g.vcf.gz.tbi, called/T79.contig-group-3.g.done log: logs/gatk/haplotypecaller/T79.contig-group-3.log jobid: 1787 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-3.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_8565.contig-group-22.g.vcf.gz, called/N_8565.contig-group-22.g.vcf.gz.tbi, called/N_8565.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-22.log jobid: 3585 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1158.contig-group-21.g.vcf.gz, called/N_1158.contig-group-21.g.vcf.gz.tbi, called/N_1158.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-21.log jobid: 3432 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_8171.contig-group-0.g.vcf.gz, called/N_8171.contig-group-0.g.vcf.gz.tbi, called/N_8171.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-0.log jobid: 1440 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1386.contig-group-25.g.vcf.gz, called/N_1386.contig-group-25.g.vcf.gz.tbi, called/N_1386.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-25.log jobid: 3822 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_8171.contig-group-23.g.vcf.gz, called/N_8171.contig-group-23.g.vcf.gz.tbi, called/N_8171.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-23.log jobid: 3678 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T180.contig-group-21.g.vcf.gz, called/T180.contig-group-21.g.vcf.gz.tbi, called/T180.contig-group-21.g.done log: logs/gatk/haplotypecaller/T180.contig-group-21.log jobid: 3500 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-21.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_83.contig-group-11.g.vcf.gz, called/N_83.contig-group-11.g.vcf.gz.tbi, called/N_83.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-11.log jobid: 2527 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_4843.contig-group-10.g.vcf.gz, called/N_4843.contig-group-10.g.vcf.gz.tbi, called/N_4843.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-10.log jobid: 2410 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T190.contig-group-15.g.vcf.gz, called/T190.contig-group-15.g.vcf.gz.tbi, called/T190.contig-group-15.g.done log: logs/gatk/haplotypecaller/T190.contig-group-15.log jobid: 2931 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-15.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1992_0123.contig-group-16.g.vcf.gz, called/N_1992_0123.contig-group-16.g.vcf.gz.tbi, called/N_1992_0123.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-16.log jobid: 2973 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1158.contig-group-14.g.vcf.gz, called/N_1158.contig-group-14.g.vcf.gz.tbi, called/N_1158.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-14.log jobid: 2760 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_689.contig-group-8.g.vcf.gz, called/N_689.contig-group-8.g.vcf.gz.tbi, called/N_689.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-8.log jobid: 2228 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_102.contig-group-16.g.vcf.gz, called/N_102.contig-group-16.g.vcf.gz.tbi, called/N_102.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-16.log jobid: 2948 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1386.contig-group-20.g.vcf.gz, called/N_1386.contig-group-20.g.vcf.gz.tbi, called/N_1386.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-20.log jobid: 3342 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_9449.contig-group-6.g.vcf.gz, called/N_9449.contig-group-6.g.vcf.gz.tbi, called/N_9449.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-6.log jobid: 2054 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_689.contig-group-26.g.vcf.gz, called/N_689.contig-group-26.g.vcf.gz.tbi, called/N_689.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-26.log jobid: 3956 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_5129.contig-group-18.g.vcf.gz, called/N_5129.contig-group-18.g.vcf.gz.tbi, called/N_5129.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-18.log jobid: 3184 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_8565.contig-group-17.g.vcf.gz, called/N_8565.contig-group-17.g.vcf.gz.tbi, called/N_8565.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-17.log jobid: 3105 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1386.contig-group-5.g.vcf.gz, called/N_1386.contig-group-5.g.vcf.gz.tbi, called/N_1386.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-5.log jobid: 1902 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1157.contig-group-4.g.vcf.gz, called/N_1157.contig-group-4.g.vcf.gz.tbi, called/N_1157.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-4.log jobid: 1799 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_6489.contig-group-11.g.vcf.gz, called/N_6489.contig-group-11.g.vcf.gz.tbi, called/N_6489.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-11.log jobid: 2513 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1354.contig-group-24.g.vcf.gz, called/N_1354.contig-group-24.g.vcf.gz.tbi, called/N_1354.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-24.log jobid: 3723 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1870.contig-group-6.g.vcf.gz, called/N_1870.contig-group-6.g.vcf.gz.tbi, called/N_1870.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-6.log jobid: 2005 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_8171.contig-group-24.g.vcf.gz, called/N_8171.contig-group-24.g.vcf.gz.tbi, called/N_8171.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-24.log jobid: 3774 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/T79.contig-group-16.g.vcf.gz, called/T79.contig-group-16.g.vcf.gz.tbi, called/T79.contig-group-16.g.done log: logs/gatk/haplotypecaller/T79.contig-group-16.log jobid: 3035 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-16.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1158.contig-group-9.g.vcf.gz, called/N_1158.contig-group-9.g.vcf.gz.tbi, called/N_1158.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-9.log jobid: 2280 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_9104.contig-group-7.g.vcf.gz, called/N_9104.contig-group-7.g.vcf.gz.tbi, called/N_9104.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-7.log jobid: 2149 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T79.contig-group-13.g.vcf.gz, called/T79.contig-group-13.g.vcf.gz.tbi, called/T79.contig-group-13.g.done log: logs/gatk/haplotypecaller/T79.contig-group-13.log jobid: 2747 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-13.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1927.contig-group-13.g.vcf.gz, called/N_1927.contig-group-13.g.vcf.gz.tbi, called/N_1927.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-13.log jobid: 2680 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_79.contig-group-9.g.vcf.gz, called/N_79.contig-group-9.g.vcf.gz.tbi, called/N_79.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-9.log jobid: 2331 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_8171.contig-group-13.g.vcf.gz, called/N_8171.contig-group-13.g.vcf.gz.tbi, called/N_8171.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-13.log jobid: 2718 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_690.contig-group-16.g.vcf.gz, called/N_690.contig-group-16.g.vcf.gz.tbi, called/N_690.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-16.log jobid: 2997 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T192.contig-group-10.g.vcf.gz, called/T192.contig-group-10.g.vcf.gz.tbi, called/T192.contig-group-10.g.done log: logs/gatk/haplotypecaller/T192.contig-group-10.log jobid: 2452 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-10.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_5129.contig-group-19.g.vcf.gz, called/N_5129.contig-group-19.g.vcf.gz.tbi, called/N_5129.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-19.log jobid: 3280 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_83.contig-group-4.g.vcf.gz, called/N_83.contig-group-4.g.vcf.gz.tbi, called/N_83.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-4.log jobid: 1855 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1354.contig-group-20.g.vcf.gz, called/N_1354.contig-group-20.g.vcf.gz.tbi, called/N_1354.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-20.log jobid: 3339 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1927.contig-group-11.g.vcf.gz, called/N_1927.contig-group-11.g.vcf.gz.tbi, called/N_1927.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-11.log jobid: 2488 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_6490.contig-group-26.g.vcf.gz, called/N_6490.contig-group-26.g.vcf.gz.tbi, called/N_6490.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-26.log jobid: 3954 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_4843.contig-group-22.g.vcf.gz, called/N_4843.contig-group-22.g.vcf.gz.tbi, called/N_4843.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-22.log jobid: 3562 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1992_0123.contig-group-9.g.vcf.gz, called/N_1992_0123.contig-group-9.g.vcf.gz.tbi, called/N_1992_0123.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-9.log jobid: 2301 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1609.contig-group-3.g.vcf.gz, called/N_1609.contig-group-3.g.vcf.gz.tbi, called/N_1609.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-3.log jobid: 1716 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N2005.contig-group-0.g.vcf.gz, called/N2005.contig-group-0.g.vcf.gz.tbi, called/N2005.contig-group-0.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-0.log jobid: 1322 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-0.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1386.contig-group-7.g.vcf.gz, called/N_1386.contig-group-7.g.vcf.gz.tbi, called/N_1386.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-7.log jobid: 2094 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_8171.contig-group-7.g.vcf.gz, called/N_8171.contig-group-7.g.vcf.gz.tbi, called/N_8171.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-7.log jobid: 2142 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T187.contig-group-9.g.vcf.gz, called/T187.contig-group-9.g.vcf.gz.tbi, called/T187.contig-group-9.g.done log: logs/gatk/haplotypecaller/T187.contig-group-9.log jobid: 2352 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-9.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1157.contig-group-19.g.vcf.gz, called/N_1157.contig-group-19.g.vcf.gz.tbi, called/N_1157.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-19.log jobid: 3239 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T79.contig-group-20.g.vcf.gz, called/T79.contig-group-20.g.vcf.gz.tbi, called/T79.contig-group-20.g.done log: logs/gatk/haplotypecaller/T79.contig-group-20.log jobid: 3419 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-20.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_6928.contig-group-9.g.vcf.gz, called/N_6928.contig-group-9.g.vcf.gz.tbi, called/N_6928.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-9.log jobid: 2327 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T79.contig-group-9.g.vcf.gz, called/T79.contig-group-9.g.vcf.gz.tbi, called/T79.contig-group-9.g.done log: logs/gatk/haplotypecaller/T79.contig-group-9.log jobid: 2363 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-9.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1870.contig-group-19.g.vcf.gz, called/N_1870.contig-group-19.g.vcf.gz.tbi, called/N_1870.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-19.log jobid: 3253 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_4847.contig-group-9.g.vcf.gz, called/N_4847.contig-group-9.g.vcf.gz.tbi, called/N_4847.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-9.log jobid: 2317 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_6489.contig-group-19.g.vcf.gz, called/N_6489.contig-group-19.g.vcf.gz.tbi, called/N_6489.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-19.log jobid: 3281 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_8583.contig-group-22.g.vcf.gz, called/N_8583.contig-group-22.g.vcf.gz.tbi, called/N_8583.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-22.log jobid: 3586 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T192.contig-group-13.g.vcf.gz, called/T192.contig-group-13.g.vcf.gz.tbi, called/T192.contig-group-13.g.done log: logs/gatk/haplotypecaller/T192.contig-group-13.log jobid: 2740 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-13.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1157.contig-group-6.g.vcf.gz, called/N_1157.contig-group-6.g.vcf.gz.tbi, called/N_1157.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-6.log jobid: 1991 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1992_0123.contig-group-17.g.vcf.gz, called/N_1992_0123.contig-group-17.g.vcf.gz.tbi, called/N_1992_0123.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-17.log jobid: 3069 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1158.contig-group-20.g.vcf.gz, called/N_1158.contig-group-20.g.vcf.gz.tbi, called/N_1158.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-20.log jobid: 3336 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1354.contig-group-3.g.vcf.gz, called/N_1354.contig-group-3.g.vcf.gz.tbi, called/N_1354.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-3.log jobid: 1707 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1386.contig-group-11.g.vcf.gz, called/N_1386.contig-group-11.g.vcf.gz.tbi, called/N_1386.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-11.log jobid: 2478 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1992_0123.contig-group-19.g.vcf.gz, called/N_1992_0123.contig-group-19.g.vcf.gz.tbi, called/N_1992_0123.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-19.log jobid: 3261 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T180.contig-group-2.g.vcf.gz, called/T180.contig-group-2.g.vcf.gz.tbi, called/T180.contig-group-2.g.done log: logs/gatk/haplotypecaller/T180.contig-group-2.log jobid: 1676 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-2.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_5129.contig-group-11.g.vcf.gz, called/N_5129.contig-group-11.g.vcf.gz.tbi, called/N_5129.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-11.log jobid: 2512 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_8171.contig-group-11.g.vcf.gz, called/N_8171.contig-group-11.g.vcf.gz.tbi, called/N_8171.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-11.log jobid: 2526 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_102.contig-group-15.g.vcf.gz, called/N_102.contig-group-15.g.vcf.gz.tbi, called/N_102.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-15.log jobid: 2852 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_690.contig-group-8.g.vcf.gz, called/N_690.contig-group-8.g.vcf.gz.tbi, called/N_690.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-8.log jobid: 2229 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T180.contig-group-20.g.vcf.gz, called/T180.contig-group-20.g.vcf.gz.tbi, called/T180.contig-group-20.g.done log: logs/gatk/haplotypecaller/T180.contig-group-20.log jobid: 3404 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-20.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1934_1_1_5973.contig-group-10.g.vcf.gz, called/N_1934_1_1_5973.contig-group-10.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-10.log jobid: 2395 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_689.contig-group-3.g.vcf.gz, called/N_689.contig-group-3.g.vcf.gz.tbi, called/N_689.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-3.log jobid: 1748 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_9104.contig-group-13.g.vcf.gz, called/N_9104.contig-group-13.g.vcf.gz.tbi, called/N_9104.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-13.log jobid: 2725 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_4843.contig-group-0.g.vcf.gz, called/N_4843.contig-group-0.g.vcf.gz.tbi, called/N_4843.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-0.log jobid: 1400 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T1483.contig-group-26.g.vcf.gz, called/T1483.contig-group-26.g.vcf.gz.tbi, called/T1483.contig-group-26.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-26.log jobid: 3977 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-26.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1934_1_1_5973.contig-group-4.g.vcf.gz, called/N_1934_1_1_5973.contig-group-4.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-4.log jobid: 1819 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1354.contig-group-2.g.vcf.gz, called/N_1354.contig-group-2.g.vcf.gz.tbi, called/N_1354.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-2.log jobid: 1611 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T185.contig-group-15.g.vcf.gz, called/T185.contig-group-15.g.vcf.gz.tbi, called/T185.contig-group-15.g.done log: logs/gatk/haplotypecaller/T185.contig-group-15.log jobid: 2926 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-15.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_8565.contig-group-25.g.vcf.gz, called/N_8565.contig-group-25.g.vcf.gz.tbi, called/N_8565.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-25.log jobid: 3873 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T180.contig-group-7.g.vcf.gz, called/T180.contig-group-7.g.vcf.gz.tbi, called/T180.contig-group-7.g.done log: logs/gatk/haplotypecaller/T180.contig-group-7.log jobid: 2156 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-7.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T180.contig-group-3.g.vcf.gz, called/T180.contig-group-3.g.vcf.gz.tbi, called/T180.contig-group-3.g.done log: logs/gatk/haplotypecaller/T180.contig-group-3.log jobid: 1772 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-3.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1156.contig-group-11.g.vcf.gz, called/N_1156.contig-group-11.g.vcf.gz.tbi, called/N_1156.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-11.log jobid: 2470 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1927.contig-group-9.g.vcf.gz, called/N_1927.contig-group-9.g.vcf.gz.tbi, called/N_1927.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-9.log jobid: 2296 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T72.contig-group-19.g.vcf.gz, called/T72.contig-group-19.g.vcf.gz.tbi, called/T72.contig-group-19.g.done log: logs/gatk/haplotypecaller/T72.contig-group-19.log jobid: 3322 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-19.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1870.contig-group-13.g.vcf.gz, called/N_1870.contig-group-13.g.vcf.gz.tbi, called/N_1870.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-13.log jobid: 2677 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_690.contig-group-19.g.vcf.gz, called/N_690.contig-group-19.g.vcf.gz.tbi, called/N_690.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-19.log jobid: 3285 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1354.contig-group-5.g.vcf.gz, called/N_1354.contig-group-5.g.vcf.gz.tbi, called/N_1354.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-5.log jobid: 1899 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1870.contig-group-3.g.vcf.gz, called/N_1870.contig-group-3.g.vcf.gz.tbi, called/N_1870.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-3.log jobid: 1717 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1157.contig-group-15.g.vcf.gz, called/N_1157.contig-group-15.g.vcf.gz.tbi, called/N_1157.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-15.log jobid: 2855 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_6928.contig-group-5.g.vcf.gz, called/N_6928.contig-group-5.g.vcf.gz.tbi, called/N_6928.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-5.log jobid: 1943 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_83.contig-group-12.g.vcf.gz, called/N_83.contig-group-12.g.vcf.gz.tbi, called/N_83.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-12.log jobid: 2623 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1992_0123.contig-group-23.g.vcf.gz, called/N_1992_0123.contig-group-23.g.vcf.gz.tbi, called/N_1992_0123.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-23.log jobid: 3645 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T190.contig-group-22.g.vcf.gz, called/T190.contig-group-22.g.vcf.gz.tbi, called/T190.contig-group-22.g.done log: logs/gatk/haplotypecaller/T190.contig-group-22.log jobid: 3603 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-22.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N2005.contig-group-5.g.vcf.gz, called/N2005.contig-group-5.g.vcf.gz.tbi, called/N2005.contig-group-5.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-5.log jobid: 1891 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-5.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T187.contig-group-12.g.vcf.gz, called/T187.contig-group-12.g.vcf.gz.tbi, called/T187.contig-group-12.g.done log: logs/gatk/haplotypecaller/T187.contig-group-12.log jobid: 2640 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-12.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_9449.contig-group-10.g.vcf.gz, called/N_9449.contig-group-10.g.vcf.gz.tbi, called/N_9449.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-10.log jobid: 2438 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_690.contig-group-26.g.vcf.gz, called/N_690.contig-group-26.g.vcf.gz.tbi, called/N_690.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-26.log jobid: 3957 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_6490.contig-group-1.g.vcf.gz, called/N_6490.contig-group-1.g.vcf.gz.tbi, called/N_6490.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-1.log jobid: 1554 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_8565.contig-group-1.g.vcf.gz, called/N_8565.contig-group-1.g.vcf.gz.tbi, called/N_8565.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-1.log jobid: 1569 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1157.contig-group-24.g.vcf.gz, called/N_1157.contig-group-24.g.vcf.gz.tbi, called/N_1157.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-24.log jobid: 3719 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_83.contig-group-20.g.vcf.gz, called/N_83.contig-group-20.g.vcf.gz.tbi, called/N_83.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-20.log jobid: 3391 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T72.contig-group-0.g.vcf.gz, called/T72.contig-group-0.g.vcf.gz.tbi, called/T72.contig-group-0.g.done log: logs/gatk/haplotypecaller/T72.contig-group-0.log jobid: 1496 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-0.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_5129.contig-group-21.g.vcf.gz, called/N_5129.contig-group-21.g.vcf.gz.tbi, called/N_5129.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-21.log jobid: 3472 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_8583.contig-group-26.g.vcf.gz, called/N_8583.contig-group-26.g.vcf.gz.tbi, called/N_8583.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-26.log jobid: 3970 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_351.contig-group-21.g.vcf.gz, called/N_351.contig-group-21.g.vcf.gz.tbi, called/N_351.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-21.log jobid: 3462 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_351.contig-group-8.g.vcf.gz, called/N_351.contig-group-8.g.vcf.gz.tbi, called/N_351.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-8.log jobid: 2214 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1927.contig-group-19.g.vcf.gz, called/N_1927.contig-group-19.g.vcf.gz.tbi, called/N_1927.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-19.log jobid: 3256 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_690.contig-group-1.g.vcf.gz, called/N_690.contig-group-1.g.vcf.gz.tbi, called/N_690.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-1.log jobid: 1557 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T79.contig-group-5.g.vcf.gz, called/T79.contig-group-5.g.vcf.gz.tbi, called/T79.contig-group-5.g.done log: logs/gatk/haplotypecaller/T79.contig-group-5.log jobid: 1979 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-5.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T79.contig-group-14.g.vcf.gz, called/T79.contig-group-14.g.vcf.gz.tbi, called/T79.contig-group-14.g.done log: logs/gatk/haplotypecaller/T79.contig-group-14.log jobid: 2843 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-14.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_4847.contig-group-5.g.vcf.gz, called/N_4847.contig-group-5.g.vcf.gz.tbi, called/N_4847.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-5.log jobid: 1933 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N2005.contig-group-21.g.vcf.gz, called/N2005.contig-group-21.g.vcf.gz.tbi, called/N2005.contig-group-21.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-21.log jobid: 3427 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-21.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_83.contig-group-19.g.vcf.gz, called/N_83.contig-group-19.g.vcf.gz.tbi, called/N_83.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-19.log jobid: 3295 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_102.contig-group-5.g.vcf.gz, called/N_102.contig-group-5.g.vcf.gz.tbi, called/N_102.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-5.log jobid: 1892 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T180.contig-group-17.g.vcf.gz, called/T180.contig-group-17.g.vcf.gz.tbi, called/T180.contig-group-17.g.done log: logs/gatk/haplotypecaller/T180.contig-group-17.log jobid: 3116 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-17.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N2005.contig-group-22.g.vcf.gz, called/N2005.contig-group-22.g.vcf.gz.tbi, called/N2005.contig-group-22.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-22.log jobid: 3523 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-22.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1156.contig-group-1.g.vcf.gz, called/N_1156.contig-group-1.g.vcf.gz.tbi, called/N_1156.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-1.log jobid: 1510 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1354.contig-group-1.g.vcf.gz, called/N_1354.contig-group-1.g.vcf.gz.tbi, called/N_1354.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-1.log jobid: 1515 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T72.contig-group-9.g.vcf.gz, called/T72.contig-group-9.g.vcf.gz.tbi, called/T72.contig-group-9.g.done log: logs/gatk/haplotypecaller/T72.contig-group-9.log jobid: 2362 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-9.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T192.contig-group-26.g.vcf.gz, called/T192.contig-group-26.g.vcf.gz.tbi, called/T192.contig-group-26.g.done log: logs/gatk/haplotypecaller/T192.contig-group-26.log jobid: 3988 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-26.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T187.contig-group-17.g.vcf.gz, called/T187.contig-group-17.g.vcf.gz.tbi, called/T187.contig-group-17.g.done log: logs/gatk/haplotypecaller/T187.contig-group-17.log jobid: 3120 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-17.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T185.contig-group-2.g.vcf.gz, called/T185.contig-group-2.g.vcf.gz.tbi, called/T185.contig-group-2.g.done log: logs/gatk/haplotypecaller/T185.contig-group-2.log jobid: 1678 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-2.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T79.contig-group-10.g.vcf.gz, called/T79.contig-group-10.g.vcf.gz.tbi, called/T79.contig-group-10.g.done log: logs/gatk/haplotypecaller/T79.contig-group-10.log jobid: 2459 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-10.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1870.contig-group-26.g.vcf.gz, called/N_1870.contig-group-26.g.vcf.gz.tbi, called/N_1870.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-26.log jobid: 3925 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1157.contig-group-2.g.vcf.gz, called/N_1157.contig-group-2.g.vcf.gz.tbi, called/N_1157.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-2.log jobid: 1607 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1157.contig-group-18.g.vcf.gz, called/N_1157.contig-group-18.g.vcf.gz.tbi, called/N_1157.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-18.log jobid: 3143 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T180.contig-group-0.g.vcf.gz, called/T180.contig-group-0.g.vcf.gz.tbi, called/T180.contig-group-0.g.done log: logs/gatk/haplotypecaller/T180.contig-group-0.log jobid: 1468 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-0.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_9104.contig-group-20.g.vcf.gz, called/N_9104.contig-group-20.g.vcf.gz.tbi, called/N_9104.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-20.log jobid: 3397 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1609.contig-group-14.g.vcf.gz, called/N_1609.contig-group-14.g.vcf.gz.tbi, called/N_1609.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-14.log jobid: 2772 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_102.contig-group-19.g.vcf.gz, called/N_102.contig-group-19.g.vcf.gz.tbi, called/N_102.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-19.log jobid: 3236 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_79.contig-group-11.g.vcf.gz, called/N_79.contig-group-11.g.vcf.gz.tbi, called/N_79.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-11.log jobid: 2523 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_79.contig-group-0.g.vcf.gz, called/N_79.contig-group-0.g.vcf.gz.tbi, called/N_79.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-0.log jobid: 1434 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T79.contig-group-25.g.vcf.gz, called/T79.contig-group-25.g.vcf.gz.tbi, called/T79.contig-group-25.g.done log: logs/gatk/haplotypecaller/T79.contig-group-25.log jobid: 3899 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-25.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/M5672.contig-group-1.g.vcf.gz, called/M5672.contig-group-1.g.vcf.gz.tbi, called/M5672.contig-group-1.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-1.log jobid: 1505 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-1.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_9449.contig-group-17.g.vcf.gz, called/N_9449.contig-group-17.g.vcf.gz.tbi, called/N_9449.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-17.log jobid: 3110 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T180.contig-group-9.g.vcf.gz, called/T180.contig-group-9.g.vcf.gz.tbi, called/T180.contig-group-9.g.done log: logs/gatk/haplotypecaller/T180.contig-group-9.log jobid: 2348 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-9.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1158.contig-group-13.g.vcf.gz, called/N_1158.contig-group-13.g.vcf.gz.tbi, called/N_1158.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-13.log jobid: 2664 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_9104.contig-group-18.g.vcf.gz, called/N_9104.contig-group-18.g.vcf.gz.tbi, called/N_9104.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-18.log jobid: 3205 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/M5672.contig-group-6.g.vcf.gz, called/M5672.contig-group-6.g.vcf.gz.tbi, called/M5672.contig-group-6.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-6.log jobid: 1985 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-6.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1386.contig-group-17.g.vcf.gz, called/N_1386.contig-group-17.g.vcf.gz.tbi, called/N_1386.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-17.log jobid: 3054 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T1483.contig-group-18.g.vcf.gz, called/T1483.contig-group-18.g.vcf.gz.tbi, called/T1483.contig-group-18.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-18.log jobid: 3209 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-18.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1386.contig-group-8.g.vcf.gz, called/N_1386.contig-group-8.g.vcf.gz.tbi, called/N_1386.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-8.log jobid: 2190 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T192.contig-group-19.g.vcf.gz, called/T192.contig-group-19.g.vcf.gz.tbi, called/T192.contig-group-19.g.done log: logs/gatk/haplotypecaller/T192.contig-group-19.log jobid: 3316 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-19.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T72.contig-group-14.g.vcf.gz, called/T72.contig-group-14.g.vcf.gz.tbi, called/T72.contig-group-14.g.done log: logs/gatk/haplotypecaller/T72.contig-group-14.log jobid: 2842 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-14.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_6928.contig-group-0.g.vcf.gz, called/N_6928.contig-group-0.g.vcf.gz.tbi, called/N_6928.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-0.log jobid: 1426 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T72.contig-group-4.g.vcf.gz, called/T72.contig-group-4.g.vcf.gz.tbi, called/T72.contig-group-4.g.done log: logs/gatk/haplotypecaller/T72.contig-group-4.log jobid: 1882 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-4.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_102.contig-group-23.g.vcf.gz, called/N_102.contig-group-23.g.vcf.gz.tbi, called/N_102.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-23.log jobid: 3620 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1156.contig-group-18.g.vcf.gz, called/N_1156.contig-group-18.g.vcf.gz.tbi, called/N_1156.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-18.log jobid: 3142 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_1354.contig-group-16.g.vcf.gz, called/N_1354.contig-group-16.g.vcf.gz.tbi, called/N_1354.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-16.log jobid: 2955 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/T190.contig-group-4.g.vcf.gz, called/T190.contig-group-4.g.vcf.gz.tbi, called/T190.contig-group-4.g.done log: logs/gatk/haplotypecaller/T190.contig-group-4.log jobid: 1875 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-4.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/M5672.contig-group-5.g.vcf.gz, called/M5672.contig-group-5.g.vcf.gz.tbi, called/M5672.contig-group-5.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-5.log jobid: 1889 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-5.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1934_1_1_5973.contig-group-17.g.vcf.gz, called/N_1934_1_1_5973.contig-group-17.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-17.log jobid: 3067 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_9104.contig-group-8.g.vcf.gz, called/N_9104.contig-group-8.g.vcf.gz.tbi, called/N_9104.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-8.log jobid: 2245 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T192.contig-group-24.g.vcf.gz, called/T192.contig-group-24.g.vcf.gz.tbi, called/T192.contig-group-24.g.done log: logs/gatk/haplotypecaller/T192.contig-group-24.log jobid: 3796 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-24.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1927.contig-group-12.g.vcf.gz, called/N_1927.contig-group-12.g.vcf.gz.tbi, called/N_1927.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-12.log jobid: 2584 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_4843.contig-group-18.g.vcf.gz, called/N_4843.contig-group-18.g.vcf.gz.tbi, called/N_4843.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-18.log jobid: 3178 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T196.contig-group-15.g.vcf.gz, called/T196.contig-group-15.g.vcf.gz.tbi, called/T196.contig-group-15.g.done log: logs/gatk/haplotypecaller/T196.contig-group-15.log jobid: 2935 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-15.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T192.contig-group-12.g.vcf.gz, called/T192.contig-group-12.g.vcf.gz.tbi, called/T192.contig-group-12.g.done log: logs/gatk/haplotypecaller/T192.contig-group-12.log jobid: 2644 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-12.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_1927.contig-group-15.g.vcf.gz, called/N_1927.contig-group-15.g.vcf.gz.tbi, called/N_1927.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-15.log jobid: 2872 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T79.contig-group-17.g.vcf.gz, called/T79.contig-group-17.g.vcf.gz.tbi, called/T79.contig-group-17.g.done log: logs/gatk/haplotypecaller/T79.contig-group-17.log jobid: 3131 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-17.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_6489.contig-group-13.g.vcf.gz, called/N_6489.contig-group-13.g.vcf.gz.tbi, called/N_6489.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-13.log jobid: 2705 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_6489.contig-group-17.g.vcf.gz, called/N_6489.contig-group-17.g.vcf.gz.tbi, called/N_6489.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-17.log jobid: 3089 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_351.contig-group-12.g.vcf.gz, called/N_351.contig-group-12.g.vcf.gz.tbi, called/N_351.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-12.log jobid: 2598 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1609.contig-group-5.g.vcf.gz, called/N_1609.contig-group-5.g.vcf.gz.tbi, called/N_1609.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-5.log jobid: 1908 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T180.contig-group-10.g.vcf.gz, called/T180.contig-group-10.g.vcf.gz.tbi, called/T180.contig-group-10.g.done log: logs/gatk/haplotypecaller/T180.contig-group-10.log jobid: 2444 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-10.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1934_1_1_5973.contig-group-22.g.vcf.gz, called/N_1934_1_1_5973.contig-group-22.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-22.log jobid: 3547 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1158.contig-group-8.g.vcf.gz, called/N_1158.contig-group-8.g.vcf.gz.tbi, called/N_1158.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-8.log jobid: 2184 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1992_0123.contig-group-8.g.vcf.gz, called/N_1992_0123.contig-group-8.g.vcf.gz.tbi, called/N_1992_0123.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-8.log jobid: 2205 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T196.contig-group-8.g.vcf.gz, called/T196.contig-group-8.g.vcf.gz.tbi, called/T196.contig-group-8.g.done log: logs/gatk/haplotypecaller/T196.contig-group-8.log jobid: 2263 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-8.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_83.contig-group-0.g.vcf.gz, called/N_83.contig-group-0.g.vcf.gz.tbi, called/N_83.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-0.log jobid: 1442 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_8583.contig-group-19.g.vcf.gz, called/N_8583.contig-group-19.g.vcf.gz.tbi, called/N_8583.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-19.log jobid: 3298 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_83.contig-group-16.g.vcf.gz, called/N_83.contig-group-16.g.vcf.gz.tbi, called/N_83.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-16.log jobid: 3007 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1156.contig-group-5.g.vcf.gz, called/N_1156.contig-group-5.g.vcf.gz.tbi, called/N_1156.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-5.log jobid: 1894 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1609.contig-group-10.g.vcf.gz, called/N_1609.contig-group-10.g.vcf.gz.tbi, called/N_1609.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-10.log jobid: 2388 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_6490.contig-group-16.g.vcf.gz, called/N_6490.contig-group-16.g.vcf.gz.tbi, called/N_6490.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-16.log jobid: 2994 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_79.contig-group-7.g.vcf.gz, called/N_79.contig-group-7.g.vcf.gz.tbi, called/N_79.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-7.log jobid: 2139 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_5129.contig-group-9.g.vcf.gz, called/N_5129.contig-group-9.g.vcf.gz.tbi, called/N_5129.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-9.log jobid: 2320 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1992_0123.contig-group-6.g.vcf.gz, called/N_1992_0123.contig-group-6.g.vcf.gz.tbi, called/N_1992_0123.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-6.log jobid: 2013 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/M5672.contig-group-16.g.vcf.gz, called/M5672.contig-group-16.g.vcf.gz.tbi, called/M5672.contig-group-16.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-16.log jobid: 2945 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-16.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_8583.contig-group-15.g.vcf.gz, called/N_8583.contig-group-15.g.vcf.gz.tbi, called/N_8583.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-15.log jobid: 2914 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_4847.contig-group-11.g.vcf.gz, called/N_4847.contig-group-11.g.vcf.gz.tbi, called/N_4847.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-11.log jobid: 2509 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_5129.contig-group-13.g.vcf.gz, called/N_5129.contig-group-13.g.vcf.gz.tbi, called/N_5129.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-13.log jobid: 2704 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_8583.contig-group-16.g.vcf.gz, called/N_8583.contig-group-16.g.vcf.gz.tbi, called/N_8583.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-16.log jobid: 3010 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1870.contig-group-5.g.vcf.gz, called/N_1870.contig-group-5.g.vcf.gz.tbi, called/N_1870.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-5.log jobid: 1909 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_8565.contig-group-2.g.vcf.gz, called/N_8565.contig-group-2.g.vcf.gz.tbi, called/N_8565.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-2.log jobid: 1665 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1386.contig-group-4.g.vcf.gz, called/N_1386.contig-group-4.g.vcf.gz.tbi, called/N_1386.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-4.log jobid: 1806 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T190.contig-group-24.g.vcf.gz, called/T190.contig-group-24.g.vcf.gz.tbi, called/T190.contig-group-24.g.done log: logs/gatk/haplotypecaller/T190.contig-group-24.log jobid: 3795 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-24.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T190.contig-group-21.g.vcf.gz, called/T190.contig-group-21.g.vcf.gz.tbi, called/T190.contig-group-21.g.done log: logs/gatk/haplotypecaller/T190.contig-group-21.log jobid: 3507 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-21.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N2005.contig-group-8.g.vcf.gz, called/N2005.contig-group-8.g.vcf.gz.tbi, called/N2005.contig-group-8.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-8.log jobid: 2179 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-8.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T190.contig-group-3.g.vcf.gz, called/T190.contig-group-3.g.vcf.gz.tbi, called/T190.contig-group-3.g.done log: logs/gatk/haplotypecaller/T190.contig-group-3.log jobid: 1779 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-3.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_5129.contig-group-3.g.vcf.gz, called/N_5129.contig-group-3.g.vcf.gz.tbi, called/N_5129.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-3.log jobid: 1744 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1870.contig-group-0.g.vcf.gz, called/N_1870.contig-group-0.g.vcf.gz.tbi, called/N_1870.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-0.log jobid: 1358 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/T79.contig-group-6.g.vcf.gz, called/T79.contig-group-6.g.vcf.gz.tbi, called/T79.contig-group-6.g.done log: logs/gatk/haplotypecaller/T79.contig-group-6.log jobid: 2075 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-6.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_83.contig-group-15.g.vcf.gz, called/N_83.contig-group-15.g.vcf.gz.tbi, called/N_83.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-15.log jobid: 2911 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_102.contig-group-22.g.vcf.gz, called/N_102.contig-group-22.g.vcf.gz.tbi, called/N_102.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-22.log jobid: 3524 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_8565.contig-group-5.g.vcf.gz, called/N_8565.contig-group-5.g.vcf.gz.tbi, called/N_8565.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-5.log jobid: 1953 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_689.contig-group-22.g.vcf.gz, called/N_689.contig-group-22.g.vcf.gz.tbi, called/N_689.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-22.log jobid: 3572 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1609.contig-group-0.g.vcf.gz, called/N_1609.contig-group-0.g.vcf.gz.tbi, called/N_1609.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-0.log jobid: 1356 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T196.contig-group-9.g.vcf.gz, called/T196.contig-group-9.g.vcf.gz.tbi, called/T196.contig-group-9.g.done log: logs/gatk/haplotypecaller/T196.contig-group-9.log jobid: 2359 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-9.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1354.contig-group-17.g.vcf.gz, called/N_1354.contig-group-17.g.vcf.gz.tbi, called/N_1354.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-17.log jobid: 3051 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_6928.contig-group-4.g.vcf.gz, called/N_6928.contig-group-4.g.vcf.gz.tbi, called/N_6928.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-4.log jobid: 1847 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_689.contig-group-7.g.vcf.gz, called/N_689.contig-group-7.g.vcf.gz.tbi, called/N_689.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-7.log jobid: 2132 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_6489.contig-group-10.g.vcf.gz, called/N_6489.contig-group-10.g.vcf.gz.tbi, called/N_6489.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-10.log jobid: 2417 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/M5672.contig-group-23.g.vcf.gz, called/M5672.contig-group-23.g.vcf.gz.tbi, called/M5672.contig-group-23.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-23.log jobid: 3617 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-23.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_689.contig-group-25.g.vcf.gz, called/N_689.contig-group-25.g.vcf.gz.tbi, called/N_689.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-25.log jobid: 3860 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_4843.contig-group-7.g.vcf.gz, called/N_4843.contig-group-7.g.vcf.gz.tbi, called/N_4843.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-7.log jobid: 2122 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_102.contig-group-13.g.vcf.gz, called/N_102.contig-group-13.g.vcf.gz.tbi, called/N_102.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-13.log jobid: 2660 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_690.contig-group-9.g.vcf.gz, called/N_690.contig-group-9.g.vcf.gz.tbi, called/N_690.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-9.log jobid: 2325 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_2003_5409.contig-group-2.g.vcf.gz, called/N_2003_5409.contig-group-2.g.vcf.gz.tbi, called/N_2003_5409.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-2.log jobid: 1634 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N2005.contig-group-1.g.vcf.gz, called/N2005.contig-group-1.g.vcf.gz.tbi, called/N2005.contig-group-1.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-1.log jobid: 1507 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-1.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_8171.contig-group-15.g.vcf.gz, called/N_8171.contig-group-15.g.vcf.gz.tbi, called/N_8171.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-15.log jobid: 2910 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1934_1_1_5973.contig-group-6.g.vcf.gz, called/N_1934_1_1_5973.contig-group-6.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-6.log jobid: 2011 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_6928.contig-group-22.g.vcf.gz, called/N_6928.contig-group-22.g.vcf.gz.tbi, called/N_6928.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-22.log jobid: 3575 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_5129.contig-group-25.g.vcf.gz, called/N_5129.contig-group-25.g.vcf.gz.tbi, called/N_5129.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-25.log jobid: 3856 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1156.contig-group-4.g.vcf.gz, called/N_1156.contig-group-4.g.vcf.gz.tbi, called/N_1156.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-4.log jobid: 1798 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T185.contig-group-7.g.vcf.gz, called/T185.contig-group-7.g.vcf.gz.tbi, called/T185.contig-group-7.g.done log: logs/gatk/haplotypecaller/T185.contig-group-7.log jobid: 2158 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-7.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T190.contig-group-10.g.vcf.gz, called/T190.contig-group-10.g.vcf.gz.tbi, called/T190.contig-group-10.g.done log: logs/gatk/haplotypecaller/T190.contig-group-10.log jobid: 2451 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-10.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_5129.contig-group-12.g.vcf.gz, called/N_5129.contig-group-12.g.vcf.gz.tbi, called/N_5129.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-12.log jobid: 2608 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T192.contig-group-3.g.vcf.gz, called/T192.contig-group-3.g.vcf.gz.tbi, called/T192.contig-group-3.g.done log: logs/gatk/haplotypecaller/T192.contig-group-3.log jobid: 1780 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-3.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_9449.contig-group-13.g.vcf.gz, called/N_9449.contig-group-13.g.vcf.gz.tbi, called/N_9449.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-13.log jobid: 2726 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T1483.contig-group-1.g.vcf.gz, called/T1483.contig-group-1.g.vcf.gz.tbi, called/T1483.contig-group-1.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-1.log jobid: 1577 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-1.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/M5672.contig-group-26.g.vcf.gz, called/M5672.contig-group-26.g.vcf.gz.tbi, called/M5672.contig-group-26.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-26.log jobid: 3905 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-26.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1156.contig-group-14.g.vcf.gz, called/N_1156.contig-group-14.g.vcf.gz.tbi, called/N_1156.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-14.log jobid: 2758 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T185.contig-group-13.g.vcf.gz, called/T185.contig-group-13.g.vcf.gz.tbi, called/T185.contig-group-13.g.done log: logs/gatk/haplotypecaller/T185.contig-group-13.log jobid: 2734 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-13.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T185.contig-group-3.g.vcf.gz, called/T185.contig-group-3.g.vcf.gz.tbi, called/T185.contig-group-3.g.done log: logs/gatk/haplotypecaller/T185.contig-group-3.log jobid: 1774 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-3.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_2003_5409.contig-group-10.g.vcf.gz, called/N_2003_5409.contig-group-10.g.vcf.gz.tbi, called/N_2003_5409.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-10.log jobid: 2402 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N2005.contig-group-15.g.vcf.gz, called/N2005.contig-group-15.g.vcf.gz.tbi, called/N2005.contig-group-15.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-15.log jobid: 2851 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-15.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T1483.contig-group-7.g.vcf.gz, called/T1483.contig-group-7.g.vcf.gz.tbi, called/T1483.contig-group-7.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-7.log jobid: 2153 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-7.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/T187.contig-group-26.g.vcf.gz, called/T187.contig-group-26.g.vcf.gz.tbi, called/T187.contig-group-26.g.done log: logs/gatk/haplotypecaller/T187.contig-group-26.log jobid: 3984 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-26.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T196.contig-group-5.g.vcf.gz, called/T196.contig-group-5.g.vcf.gz.tbi, called/T196.contig-group-5.g.done log: logs/gatk/haplotypecaller/T196.contig-group-5.log jobid: 1975 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-5.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_351.contig-group-4.g.vcf.gz, called/N_351.contig-group-4.g.vcf.gz.tbi, called/N_351.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-4.log jobid: 1830 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_6928.contig-group-17.g.vcf.gz, called/N_6928.contig-group-17.g.vcf.gz.tbi, called/N_6928.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-17.log jobid: 3095 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_2003_5409.contig-group-19.g.vcf.gz, called/N_2003_5409.contig-group-19.g.vcf.gz.tbi, called/N_2003_5409.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-19.log jobid: 3266 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_1927.contig-group-20.g.vcf.gz, called/N_1927.contig-group-20.g.vcf.gz.tbi, called/N_1927.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-20.log jobid: 3352 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T187.contig-group-1.g.vcf.gz, called/T187.contig-group-1.g.vcf.gz.tbi, called/T187.contig-group-1.g.done log: logs/gatk/haplotypecaller/T187.contig-group-1.log jobid: 1584 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-1.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_1158.contig-group-17.g.vcf.gz, called/N_1158.contig-group-17.g.vcf.gz.tbi, called/N_1158.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-17.log jobid: 3048 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_79.contig-group-21.g.vcf.gz, called/N_79.contig-group-21.g.vcf.gz.tbi, called/N_79.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-21.log jobid: 3483 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_9104.contig-group-12.g.vcf.gz, called/N_9104.contig-group-12.g.vcf.gz.tbi, called/N_9104.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-12.log jobid: 2629 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T72.contig-group-22.g.vcf.gz, called/T72.contig-group-22.g.vcf.gz.tbi, called/T72.contig-group-22.g.done log: logs/gatk/haplotypecaller/T72.contig-group-22.log jobid: 3610 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-22.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_6490.contig-group-12.g.vcf.gz, called/N_6490.contig-group-12.g.vcf.gz.tbi, called/N_6490.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-12.log jobid: 2610 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_83.contig-group-17.g.vcf.gz, called/N_83.contig-group-17.g.vcf.gz.tbi, called/N_83.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-17.log jobid: 3103 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T196.contig-group-3.g.vcf.gz, called/T196.contig-group-3.g.vcf.gz.tbi, called/T196.contig-group-3.g.done log: logs/gatk/haplotypecaller/T196.contig-group-3.log jobid: 1783 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-3.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_1934_1_1_5973.contig-group-2.g.vcf.gz, called/N_1934_1_1_5973.contig-group-2.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-2.log jobid: 1627 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_6490.contig-group-24.g.vcf.gz, called/N_6490.contig-group-24.g.vcf.gz.tbi, called/N_6490.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-24.log jobid: 3762 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1927.contig-group-22.g.vcf.gz, called/N_1927.contig-group-22.g.vcf.gz.tbi, called/N_1927.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-22.log jobid: 3544 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_102.contig-group-11.g.vcf.gz, called/N_102.contig-group-11.g.vcf.gz.tbi, called/N_102.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-11.log jobid: 2468 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T79.contig-group-18.g.vcf.gz, called/T79.contig-group-18.g.vcf.gz.tbi, called/T79.contig-group-18.g.done log: logs/gatk/haplotypecaller/T79.contig-group-18.log jobid: 3227 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-18.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_6490.contig-group-11.g.vcf.gz, called/N_6490.contig-group-11.g.vcf.gz.tbi, called/N_6490.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-11.log jobid: 2514 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1934_1_1_5973.contig-group-1.g.vcf.gz, called/N_1934_1_1_5973.contig-group-1.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-1.log jobid: 1531 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_83.contig-group-25.g.vcf.gz, called/N_83.contig-group-25.g.vcf.gz.tbi, called/N_83.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-25.log jobid: 3871 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1386.contig-group-18.g.vcf.gz, called/N_1386.contig-group-18.g.vcf.gz.tbi, called/N_1386.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-18.log jobid: 3150 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1158.contig-group-25.g.vcf.gz, called/N_1158.contig-group-25.g.vcf.gz.tbi, called/N_1158.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-25.log jobid: 3816 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_351.contig-group-7.g.vcf.gz, called/N_351.contig-group-7.g.vcf.gz.tbi, called/N_351.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-7.log jobid: 2118 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T192.contig-group-14.g.vcf.gz, called/T192.contig-group-14.g.vcf.gz.tbi, called/T192.contig-group-14.g.done log: logs/gatk/haplotypecaller/T192.contig-group-14.log jobid: 2836 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-14.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_4847.contig-group-10.g.vcf.gz, called/N_4847.contig-group-10.g.vcf.gz.tbi, called/N_4847.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-10.log jobid: 2413 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_83.contig-group-24.g.vcf.gz, called/N_83.contig-group-24.g.vcf.gz.tbi, called/N_83.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-24.log jobid: 3775 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_6490.contig-group-0.g.vcf.gz, called/N_6490.contig-group-0.g.vcf.gz.tbi, called/N_6490.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-0.log jobid: 1416 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1927.contig-group-8.g.vcf.gz, called/N_1927.contig-group-8.g.vcf.gz.tbi, called/N_1927.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-8.log jobid: 2200 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_6489.contig-group-3.g.vcf.gz, called/N_6489.contig-group-3.g.vcf.gz.tbi, called/N_6489.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-3.log jobid: 1745 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T79.contig-group-23.g.vcf.gz, called/T79.contig-group-23.g.vcf.gz.tbi, called/T79.contig-group-23.g.done log: logs/gatk/haplotypecaller/T79.contig-group-23.log jobid: 3707 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-23.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N2005.contig-group-14.g.vcf.gz, called/N2005.contig-group-14.g.vcf.gz.tbi, called/N2005.contig-group-14.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-14.log jobid: 2755 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-14.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N2005.contig-group-20.g.vcf.gz, called/N2005.contig-group-20.g.vcf.gz.tbi, called/N2005.contig-group-20.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-20.log jobid: 3331 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-20.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1158.contig-group-6.g.vcf.gz, called/N_1158.contig-group-6.g.vcf.gz.tbi, called/N_1158.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-6.log jobid: 1992 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1992_0123.contig-group-18.g.vcf.gz, called/N_1992_0123.contig-group-18.g.vcf.gz.tbi, called/N_1992_0123.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-18.log jobid: 3165 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_8171.contig-group-22.g.vcf.gz, called/N_8171.contig-group-22.g.vcf.gz.tbi, called/N_8171.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-22.log jobid: 3582 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_6490.contig-group-5.g.vcf.gz, called/N_6490.contig-group-5.g.vcf.gz.tbi, called/N_6490.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-5.log jobid: 1938 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T192.contig-group-8.g.vcf.gz, called/T192.contig-group-8.g.vcf.gz.tbi, called/T192.contig-group-8.g.done log: logs/gatk/haplotypecaller/T192.contig-group-8.log jobid: 2260 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-8.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1386.contig-group-0.g.vcf.gz, called/N_1386.contig-group-0.g.vcf.gz.tbi, called/N_1386.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-0.log jobid: 1344 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1609.contig-group-25.g.vcf.gz, called/N_1609.contig-group-25.g.vcf.gz.tbi, called/N_1609.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-25.log jobid: 3828 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T192.contig-group-22.g.vcf.gz, called/T192.contig-group-22.g.vcf.gz.tbi, called/T192.contig-group-22.g.done log: logs/gatk/haplotypecaller/T192.contig-group-22.log jobid: 3604 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-22.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/T1483.contig-group-3.g.vcf.gz, called/T1483.contig-group-3.g.vcf.gz.tbi, called/T1483.contig-group-3.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-3.log jobid: 1769 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-3.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1386.contig-group-22.g.vcf.gz, called/N_1386.contig-group-22.g.vcf.gz.tbi, called/N_1386.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-22.log jobid: 3534 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_8171.contig-group-17.g.vcf.gz, called/N_8171.contig-group-17.g.vcf.gz.tbi, called/N_8171.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-17.log jobid: 3102 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_79.contig-group-25.g.vcf.gz, called/N_79.contig-group-25.g.vcf.gz.tbi, called/N_79.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-25.log jobid: 3867 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_689.contig-group-6.g.vcf.gz, called/N_689.contig-group-6.g.vcf.gz.tbi, called/N_689.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-6.log jobid: 2036 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1354.contig-group-13.g.vcf.gz, called/N_1354.contig-group-13.g.vcf.gz.tbi, called/N_1354.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-13.log jobid: 2667 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_102.contig-group-1.g.vcf.gz, called/N_102.contig-group-1.g.vcf.gz.tbi, called/N_102.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-1.log jobid: 1508 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1158.contig-group-23.g.vcf.gz, called/N_1158.contig-group-23.g.vcf.gz.tbi, called/N_1158.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-23.log jobid: 3624 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_689.contig-group-0.g.vcf.gz, called/N_689.contig-group-0.g.vcf.gz.tbi, called/N_689.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-0.log jobid: 1420 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1158.contig-group-7.g.vcf.gz, called/N_1158.contig-group-7.g.vcf.gz.tbi, called/N_1158.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-7.log jobid: 2088 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1156.contig-group-24.g.vcf.gz, called/N_1156.contig-group-24.g.vcf.gz.tbi, called/N_1156.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-24.log jobid: 3718 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1609.contig-group-6.g.vcf.gz, called/N_1609.contig-group-6.g.vcf.gz.tbi, called/N_1609.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-6.log jobid: 2004 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_8565.contig-group-21.g.vcf.gz, called/N_8565.contig-group-21.g.vcf.gz.tbi, called/N_8565.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-21.log jobid: 3489 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T1483.contig-group-17.g.vcf.gz, called/T1483.contig-group-17.g.vcf.gz.tbi, called/T1483.contig-group-17.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-17.log jobid: 3113 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-17.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N2005.contig-group-18.g.vcf.gz, called/N2005.contig-group-18.g.vcf.gz.tbi, called/N2005.contig-group-18.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-18.log jobid: 3139 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-18.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_1156.contig-group-25.g.vcf.gz, called/N_1156.contig-group-25.g.vcf.gz.tbi, called/N_1156.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-25.log jobid: 3814 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T185.contig-group-25.g.vcf.gz, called/T185.contig-group-25.g.vcf.gz.tbi, called/T185.contig-group-25.g.done log: logs/gatk/haplotypecaller/T185.contig-group-25.log jobid: 3886 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-25.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_6928.contig-group-18.g.vcf.gz, called/N_6928.contig-group-18.g.vcf.gz.tbi, called/N_6928.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-18.log jobid: 3191 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1354.contig-group-7.g.vcf.gz, called/N_1354.contig-group-7.g.vcf.gz.tbi, called/N_1354.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-7.log jobid: 2091 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_2003_5409.contig-group-11.g.vcf.gz, called/N_2003_5409.contig-group-11.g.vcf.gz.tbi, called/N_2003_5409.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-11.log jobid: 2498 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_9449.contig-group-20.g.vcf.gz, called/N_9449.contig-group-20.g.vcf.gz.tbi, called/N_9449.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-20.log jobid: 3398 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/T187.contig-group-5.g.vcf.gz, called/T187.contig-group-5.g.vcf.gz.tbi, called/T187.contig-group-5.g.done log: logs/gatk/haplotypecaller/T187.contig-group-5.log jobid: 1968 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-5.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1934_1_1_5973.contig-group-24.g.vcf.gz, called/N_1934_1_1_5973.contig-group-24.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-24.log jobid: 3739 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T79.contig-group-1.g.vcf.gz, called/T79.contig-group-1.g.vcf.gz.tbi, called/T79.contig-group-1.g.done log: logs/gatk/haplotypecaller/T79.contig-group-1.log jobid: 1595 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-1.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T180.contig-group-14.g.vcf.gz, called/T180.contig-group-14.g.vcf.gz.tbi, called/T180.contig-group-14.g.done log: logs/gatk/haplotypecaller/T180.contig-group-14.log jobid: 2828 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-14.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T180.contig-group-13.g.vcf.gz, called/T180.contig-group-13.g.vcf.gz.tbi, called/T180.contig-group-13.g.done log: logs/gatk/haplotypecaller/T180.contig-group-13.log jobid: 2732 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-13.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/M5672.contig-group-14.g.vcf.gz, called/M5672.contig-group-14.g.vcf.gz.tbi, called/M5672.contig-group-14.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-14.log jobid: 2753 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-14.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_4847.contig-group-16.g.vcf.gz, called/N_4847.contig-group-16.g.vcf.gz.tbi, called/N_4847.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-16.log jobid: 2989 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_9104.contig-group-17.g.vcf.gz, called/N_9104.contig-group-17.g.vcf.gz.tbi, called/N_9104.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-17.log jobid: 3109 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1157.contig-group-0.g.vcf.gz, called/N_1157.contig-group-0.g.vcf.gz.tbi, called/N_1157.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-0.log jobid: 1330 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_351.contig-group-20.g.vcf.gz, called/N_351.contig-group-20.g.vcf.gz.tbi, called/N_351.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-20.log jobid: 3366 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/M5672.contig-group-8.g.vcf.gz, called/M5672.contig-group-8.g.vcf.gz.tbi, called/M5672.contig-group-8.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-8.log jobid: 2177 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-8.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_1158.contig-group-3.g.vcf.gz, called/N_1158.contig-group-3.g.vcf.gz.tbi, called/N_1158.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-3.log jobid: 1704 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T192.contig-group-1.g.vcf.gz, called/T192.contig-group-1.g.vcf.gz.tbi, called/T192.contig-group-1.g.done log: logs/gatk/haplotypecaller/T192.contig-group-1.log jobid: 1588 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-1.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T72.bam, dedup/T72.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T72.contig-group-10.g.vcf.gz, called/T72.contig-group-10.g.vcf.gz.tbi, called/T72.contig-group-10.g.done log: logs/gatk/haplotypecaller/T72.contig-group-10.log jobid: 2458 benchmark: benchmarks/gatk/haplotypecaller/T72.contig-group-10.bench.log reason: Input files updated by another job: dedup/T72.bam.bai wildcards: sample=T72, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T185.contig-group-1.g.vcf.gz, called/T185.contig-group-1.g.vcf.gz.tbi, called/T185.contig-group-1.g.done log: logs/gatk/haplotypecaller/T185.contig-group-1.log jobid: 1582 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-1.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_9449.contig-group-12.g.vcf.gz, called/N_9449.contig-group-12.g.vcf.gz.tbi, called/N_9449.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-12.log jobid: 2630 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1934_1_1_5973.contig-group-5.g.vcf.gz, called/N_1934_1_1_5973.contig-group-5.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-5.log jobid: 1915 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_8171.contig-group-19.g.vcf.gz, called/N_8171.contig-group-19.g.vcf.gz.tbi, called/N_8171.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-19.log jobid: 3294 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_4843.contig-group-23.g.vcf.gz, called/N_4843.contig-group-23.g.vcf.gz.tbi, called/N_4843.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-23.log jobid: 3658 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_8171.contig-group-16.g.vcf.gz, called/N_8171.contig-group-16.g.vcf.gz.tbi, called/N_8171.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-16.log jobid: 3006 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T1483.contig-group-22.g.vcf.gz, called/T1483.contig-group-22.g.vcf.gz.tbi, called/T1483.contig-group-22.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-22.log jobid: 3593 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-22.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T1483.contig-group-20.g.vcf.gz, called/T1483.contig-group-20.g.vcf.gz.tbi, called/T1483.contig-group-20.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-20.log jobid: 3401 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-20.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:42 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:42 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_8565.contig-group-0.g.vcf.gz, called/N_8565.contig-group-0.g.vcf.gz.tbi, called/N_8565.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-0.log jobid: 1446 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_5129.contig-group-23.g.vcf.gz, called/N_5129.contig-group-23.g.vcf.gz.tbi, called/N_5129.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-23.log jobid: 3664 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_689.contig-group-23.g.vcf.gz, called/N_689.contig-group-23.g.vcf.gz.tbi, called/N_689.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-23.log jobid: 3668 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1934_1_1_5973.contig-group-21.g.vcf.gz, called/N_1934_1_1_5973.contig-group-21.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-21.log jobid: 3451 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_689.contig-group-24.g.vcf.gz, called/N_689.contig-group-24.g.vcf.gz.tbi, called/N_689.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-24.log jobid: 3764 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1934_1_1_5973.contig-group-11.g.vcf.gz, called/N_1934_1_1_5973.contig-group-11.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-11.log jobid: 2491 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_8565.contig-group-16.g.vcf.gz, called/N_8565.contig-group-16.g.vcf.gz.tbi, called/N_8565.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-16.log jobid: 3009 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1934_1_1_5973.contig-group-8.g.vcf.gz, called/N_1934_1_1_5973.contig-group-8.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-8.log jobid: 2203 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_4843.contig-group-21.g.vcf.gz, called/N_4843.contig-group-21.g.vcf.gz.tbi, called/N_4843.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-21.log jobid: 3466 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_4847.contig-group-17.g.vcf.gz, called/N_4847.contig-group-17.g.vcf.gz.tbi, called/N_4847.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-17.log jobid: 3085 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_4843.contig-group-15.g.vcf.gz, called/N_4843.contig-group-15.g.vcf.gz.tbi, called/N_4843.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-15.log jobid: 2890 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1992_0123.contig-group-26.g.vcf.gz, called/N_1992_0123.contig-group-26.g.vcf.gz.tbi, called/N_1992_0123.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-26.log jobid: 3933 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1934_1_1_5973.contig-group-14.g.vcf.gz, called/N_1934_1_1_5973.contig-group-14.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-14.log jobid: 2779 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_9449.contig-group-7.g.vcf.gz, called/N_9449.contig-group-7.g.vcf.gz.tbi, called/N_9449.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-7.log jobid: 2150 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_6489.contig-group-20.g.vcf.gz, called/N_6489.contig-group-20.g.vcf.gz.tbi, called/N_6489.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-20.log jobid: 3377 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_1870.contig-group-24.g.vcf.gz, called/N_1870.contig-group-24.g.vcf.gz.tbi, called/N_1870.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-24.log jobid: 3733 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1992_0123.contig-group-14.g.vcf.gz, called/N_1992_0123.contig-group-14.g.vcf.gz.tbi, called/N_1992_0123.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-14.log jobid: 2781 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_6490.contig-group-23.g.vcf.gz, called/N_6490.contig-group-23.g.vcf.gz.tbi, called/N_6490.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-23.log jobid: 3666 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_689.contig-group-4.g.vcf.gz, called/N_689.contig-group-4.g.vcf.gz.tbi, called/N_689.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-4.log jobid: 1844 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_6489.contig-group-6.g.vcf.gz, called/N_6489.contig-group-6.g.vcf.gz.tbi, called/N_6489.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-6.log jobid: 2033 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_690.contig-group-14.g.vcf.gz, called/N_690.contig-group-14.g.vcf.gz.tbi, called/N_690.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-14.log jobid: 2805 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T187.contig-group-2.g.vcf.gz, called/T187.contig-group-2.g.vcf.gz.tbi, called/T187.contig-group-2.g.done log: logs/gatk/haplotypecaller/T187.contig-group-2.log jobid: 1680 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-2.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_8565.contig-group-4.g.vcf.gz, called/N_8565.contig-group-4.g.vcf.gz.tbi, called/N_8565.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-4.log jobid: 1857 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_2003_5409.contig-group-1.g.vcf.gz, called/N_2003_5409.contig-group-1.g.vcf.gz.tbi, called/N_2003_5409.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-1.log jobid: 1538 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T1483.contig-group-11.g.vcf.gz, called/T1483.contig-group-11.g.vcf.gz.tbi, called/T1483.contig-group-11.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-11.log jobid: 2537 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-11.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1157.contig-group-7.g.vcf.gz, called/N_1157.contig-group-7.g.vcf.gz.tbi, called/N_1157.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-7.log jobid: 2087 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_4843.contig-group-25.g.vcf.gz, called/N_4843.contig-group-25.g.vcf.gz.tbi, called/N_4843.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-25.log jobid: 3850 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_1386.contig-group-14.g.vcf.gz, called/N_1386.contig-group-14.g.vcf.gz.tbi, called/N_1386.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-14.log jobid: 2766 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_5129.contig-group-10.g.vcf.gz, called/N_5129.contig-group-10.g.vcf.gz.tbi, called/N_5129.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-10.log jobid: 2416 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_1992_0123.contig-group-4.g.vcf.gz, called/N_1992_0123.contig-group-4.g.vcf.gz.tbi, called/N_1992_0123.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-4.log jobid: 1821 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1609.contig-group-7.g.vcf.gz, called/N_1609.contig-group-7.g.vcf.gz.tbi, called/N_1609.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-7.log jobid: 2100 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/T180.contig-group-12.g.vcf.gz, called/T180.contig-group-12.g.vcf.gz.tbi, called/T180.contig-group-12.g.done log: logs/gatk/haplotypecaller/T180.contig-group-12.log jobid: 2636 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-12.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1934_1_1_5973.bam, dedup/N_1934_1_1_5973.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1934_1_1_5973.contig-group-9.g.vcf.gz, called/N_1934_1_1_5973.contig-group-9.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-9.log jobid: 2299 benchmark: benchmarks/gatk/haplotypecaller/N_1934_1_1_5973.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1934_1_1_5973.bam.bai wildcards: sample=N_1934_1_1_5973, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T196.contig-group-1.g.vcf.gz, called/T196.contig-group-1.g.vcf.gz.tbi, called/T196.contig-group-1.g.done log: logs/gatk/haplotypecaller/T196.contig-group-1.log jobid: 1591 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-1.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_4847.contig-group-14.g.vcf.gz, called/N_4847.contig-group-14.g.vcf.gz.tbi, called/N_4847.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-14.log jobid: 2797 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1927.contig-group-0.g.vcf.gz, called/N_1927.contig-group-0.g.vcf.gz.tbi, called/N_1927.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-0.log jobid: 1364 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1870.bam, dedup/N_1870.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1870.contig-group-12.g.vcf.gz, called/N_1870.contig-group-12.g.vcf.gz.tbi, called/N_1870.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1870.contig-group-12.log jobid: 2581 benchmark: benchmarks/gatk/haplotypecaller/N_1870.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1870.bam.bai wildcards: sample=N_1870, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_6490.contig-group-25.g.vcf.gz, called/N_6490.contig-group-25.g.vcf.gz.tbi, called/N_6490.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-25.log jobid: 3858 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T187.contig-group-11.g.vcf.gz, called/T187.contig-group-11.g.vcf.gz.tbi, called/T187.contig-group-11.g.done log: logs/gatk/haplotypecaller/T187.contig-group-11.log jobid: 2544 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-11.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/T196.contig-group-11.g.vcf.gz, called/T196.contig-group-11.g.vcf.gz.tbi, called/T196.contig-group-11.g.done log: logs/gatk/haplotypecaller/T196.contig-group-11.log jobid: 2551 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-11.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/T1483.contig-group-2.g.vcf.gz, called/T1483.contig-group-2.g.vcf.gz.tbi, called/T1483.contig-group-2.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-2.log jobid: 1673 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-2.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_8583.contig-group-7.g.vcf.gz, called/N_8583.contig-group-7.g.vcf.gz.tbi, called/N_8583.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-7.log jobid: 2146 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_690.contig-group-6.g.vcf.gz, called/N_690.contig-group-6.g.vcf.gz.tbi, called/N_690.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-6.log jobid: 2037 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/N_8565.contig-group-24.g.vcf.gz, called/N_8565.contig-group-24.g.vcf.gz.tbi, called/N_8565.contig-group-24.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-24.log jobid: 3777 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-24.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_4847.contig-group-22.g.vcf.gz, called/N_4847.contig-group-22.g.vcf.gz.tbi, called/N_4847.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-22.log jobid: 3565 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T187.contig-group-14.g.vcf.gz, called/T187.contig-group-14.g.vcf.gz.tbi, called/T187.contig-group-14.g.done log: logs/gatk/haplotypecaller/T187.contig-group-14.log jobid: 2832 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-14.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/N_5129.contig-group-15.g.vcf.gz, called/N_5129.contig-group-15.g.vcf.gz.tbi, called/N_5129.contig-group-15.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-15.log jobid: 2896 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-15.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_8171.contig-group-20.g.vcf.gz, called/N_8171.contig-group-20.g.vcf.gz.tbi, called/N_8171.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-20.log jobid: 3390 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1354.contig-group-19.g.vcf.gz, called/N_1354.contig-group-19.g.vcf.gz.tbi, called/N_1354.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-19.log jobid: 3243 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_6489.contig-group-25.g.vcf.gz, called/N_6489.contig-group-25.g.vcf.gz.tbi, called/N_6489.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-25.log jobid: 3857 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_79.contig-group-16.g.vcf.gz, called/N_79.contig-group-16.g.vcf.gz.tbi, called/N_79.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-16.log jobid: 3003 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1156.contig-group-6.g.vcf.gz, called/N_1156.contig-group-6.g.vcf.gz.tbi, called/N_1156.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-6.log jobid: 1990 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T190.contig-group-19.g.vcf.gz, called/T190.contig-group-19.g.vcf.gz.tbi, called/T190.contig-group-19.g.done log: logs/gatk/haplotypecaller/T190.contig-group-19.log jobid: 3315 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-19.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_2003_5409.contig-group-9.g.vcf.gz, called/N_2003_5409.contig-group-9.g.vcf.gz.tbi, called/N_2003_5409.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-9.log jobid: 2306 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_690.contig-group-17.g.vcf.gz, called/N_690.contig-group-17.g.vcf.gz.tbi, called/N_690.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-17.log jobid: 3093 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_351.contig-group-9.g.vcf.gz, called/N_351.contig-group-9.g.vcf.gz.tbi, called/N_351.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-9.log jobid: 2310 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_8583.contig-group-2.g.vcf.gz, called/N_8583.contig-group-2.g.vcf.gz.tbi, called/N_8583.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-2.log jobid: 1666 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_8565.contig-group-13.g.vcf.gz, called/N_8565.contig-group-13.g.vcf.gz.tbi, called/N_8565.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-13.log jobid: 2721 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_8583.contig-group-20.g.vcf.gz, called/N_8583.contig-group-20.g.vcf.gz.tbi, called/N_8583.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-20.log jobid: 3394 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N2005.contig-group-23.g.vcf.gz, called/N2005.contig-group-23.g.vcf.gz.tbi, called/N2005.contig-group-23.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-23.log jobid: 3619 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-23.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_8171.contig-group-6.g.vcf.gz, called/N_8171.contig-group-6.g.vcf.gz.tbi, called/N_8171.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-6.log jobid: 2046 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_102.contig-group-10.g.vcf.gz, called/N_102.contig-group-10.g.vcf.gz.tbi, called/N_102.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-10.log jobid: 2372 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1157.contig-group-5.g.vcf.gz, called/N_1157.contig-group-5.g.vcf.gz.tbi, called/N_1157.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-5.log jobid: 1895 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1927.contig-group-6.g.vcf.gz, called/N_1927.contig-group-6.g.vcf.gz.tbi, called/N_1927.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-6.log jobid: 2008 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1386.contig-group-13.g.vcf.gz, called/N_1386.contig-group-13.g.vcf.gz.tbi, called/N_1386.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-13.log jobid: 2670 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_689.contig-group-19.g.vcf.gz, called/N_689.contig-group-19.g.vcf.gz.tbi, called/N_689.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-19.log jobid: 3284 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_9449.contig-group-8.g.vcf.gz, called/N_9449.contig-group-8.g.vcf.gz.tbi, called/N_9449.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-8.log jobid: 2246 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/M5672.bam, dedup/M5672.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/M5672.contig-group-2.g.vcf.gz, called/M5672.contig-group-2.g.vcf.gz.tbi, called/M5672.contig-group-2.g.done log: logs/gatk/haplotypecaller/M5672.contig-group-2.log jobid: 1601 benchmark: benchmarks/gatk/haplotypecaller/M5672.contig-group-2.bench.log reason: Input files updated by another job: dedup/M5672.bam.bai wildcards: sample=M5672, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_8583.contig-group-5.g.vcf.gz, called/N_8583.contig-group-5.g.vcf.gz.tbi, called/N_8583.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-5.log jobid: 1954 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_6489.contig-group-22.g.vcf.gz, called/N_6489.contig-group-22.g.vcf.gz.tbi, called/N_6489.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-22.log jobid: 3569 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_8583.contig-group-6.g.vcf.gz, called/N_8583.contig-group-6.g.vcf.gz.tbi, called/N_8583.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-6.log jobid: 2050 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_9104.contig-group-16.g.vcf.gz, called/N_9104.contig-group-16.g.vcf.gz.tbi, called/N_9104.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-16.log jobid: 3013 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_6490.contig-group-19.g.vcf.gz, called/N_6490.contig-group-19.g.vcf.gz.tbi, called/N_6490.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-19.log jobid: 3282 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1609.contig-group-13.g.vcf.gz, called/N_1609.contig-group-13.g.vcf.gz.tbi, called/N_1609.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-13.log jobid: 2676 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T190.contig-group-13.g.vcf.gz, called/T190.contig-group-13.g.vcf.gz.tbi, called/T190.contig-group-13.g.done log: logs/gatk/haplotypecaller/T190.contig-group-13.log jobid: 2739 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-13.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_4847.contig-group-7.g.vcf.gz, called/N_4847.contig-group-7.g.vcf.gz.tbi, called/N_4847.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-7.log jobid: 2125 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1157.contig-group-8.g.vcf.gz, called/N_1157.contig-group-8.g.vcf.gz.tbi, called/N_1157.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-8.log jobid: 2183 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_690.contig-group-13.g.vcf.gz, called/N_690.contig-group-13.g.vcf.gz.tbi, called/N_690.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-13.log jobid: 2709 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/N_1156.contig-group-13.g.vcf.gz, called/N_1156.contig-group-13.g.vcf.gz.tbi, called/N_1156.contig-group-13.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-13.log jobid: 2662 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-13.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1927.bam, dedup/N_1927.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_1927.contig-group-7.g.vcf.gz, called/N_1927.contig-group-7.g.vcf.gz.tbi, called/N_1927.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_1927.contig-group-7.log jobid: 2104 benchmark: benchmarks/gatk/haplotypecaller/N_1927.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_1927.bam.bai wildcards: sample=N_1927, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_1386.contig-group-1.g.vcf.gz, called/N_1386.contig-group-1.g.vcf.gz.tbi, called/N_1386.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-1.log jobid: 1518 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/N_6489.contig-group-7.g.vcf.gz, called/N_6489.contig-group-7.g.vcf.gz.tbi, called/N_6489.contig-group-7.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-7.log jobid: 2129 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-7.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T192.contig-group-9.g.vcf.gz, called/T192.contig-group-9.g.vcf.gz.tbi, called/T192.contig-group-9.g.done log: logs/gatk/haplotypecaller/T192.contig-group-9.log jobid: 2356 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-9.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_1158.contig-group-10.g.vcf.gz, called/N_1158.contig-group-10.g.vcf.gz.tbi, called/N_1158.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-10.log jobid: 2376 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-24.bed output: called/T196.contig-group-24.g.vcf.gz, called/T196.contig-group-24.g.vcf.gz.tbi, called/T196.contig-group-24.g.done log: logs/gatk/haplotypecaller/T196.contig-group-24.log jobid: 3799 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-24.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-24 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T79.contig-group-21.g.vcf.gz, called/T79.contig-group-21.g.vcf.gz.tbi, called/T79.contig-group-21.g.done log: logs/gatk/haplotypecaller/T79.contig-group-21.log jobid: 3515 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-21.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1992_0123.bam, dedup/N_1992_0123.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1992_0123.contig-group-11.g.vcf.gz, called/N_1992_0123.contig-group-11.g.vcf.gz.tbi, called/N_1992_0123.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1992_0123.contig-group-11.log jobid: 2493 benchmark: benchmarks/gatk/haplotypecaller/N_1992_0123.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1992_0123.bam.bai wildcards: sample=N_1992_0123, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/T190.contig-group-0.g.vcf.gz, called/T190.contig-group-0.g.vcf.gz.tbi, called/T190.contig-group-0.g.done log: logs/gatk/haplotypecaller/T190.contig-group-0.log jobid: 1482 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-0.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/T187.contig-group-20.g.vcf.gz, called/T187.contig-group-20.g.vcf.gz.tbi, called/T187.contig-group-20.g.done log: logs/gatk/haplotypecaller/T187.contig-group-20.log jobid: 3408 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-20.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T180.contig-group-22.g.vcf.gz, called/T180.contig-group-22.g.vcf.gz.tbi, called/T180.contig-group-22.g.done log: logs/gatk/haplotypecaller/T180.contig-group-22.log jobid: 3596 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-22.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/T190.contig-group-23.g.vcf.gz, called/T190.contig-group-23.g.vcf.gz.tbi, called/T190.contig-group-23.g.done log: logs/gatk/haplotypecaller/T190.contig-group-23.log jobid: 3699 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-23.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/T187.contig-group-21.g.vcf.gz, called/T187.contig-group-21.g.vcf.gz.tbi, called/T187.contig-group-21.g.done log: logs/gatk/haplotypecaller/T187.contig-group-21.log jobid: 3504 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-21.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1386.contig-group-23.g.vcf.gz, called/N_1386.contig-group-23.g.vcf.gz.tbi, called/N_1386.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-23.log jobid: 3630 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8583.bam, dedup/N_8583.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-4.bed output: called/N_8583.contig-group-4.g.vcf.gz, called/N_8583.contig-group-4.g.vcf.gz.tbi, called/N_8583.contig-group-4.g.done log: logs/gatk/haplotypecaller/N_8583.contig-group-4.log jobid: 1858 benchmark: benchmarks/gatk/haplotypecaller/N_8583.contig-group-4.bench.log reason: Input files updated by another job: dedup/N_8583.bam.bai wildcards: sample=N_8583, contig=contig-group-4 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/N_1609.contig-group-8.g.vcf.gz, called/N_1609.contig-group-8.g.vcf.gz.tbi, called/N_1609.contig-group-8.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-8.log jobid: 2196 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-8.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T187.contig-group-25.g.vcf.gz, called/T187.contig-group-25.g.vcf.gz.tbi, called/T187.contig-group-25.g.done log: logs/gatk/haplotypecaller/T187.contig-group-25.log jobid: 3888 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-25.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_351.contig-group-26.g.vcf.gz, called/N_351.contig-group-26.g.vcf.gz.tbi, called/N_351.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-26.log jobid: 3942 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_2003_5409.bam, dedup/N_2003_5409.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_2003_5409.contig-group-0.g.vcf.gz, called/N_2003_5409.contig-group-0.g.vcf.gz.tbi, called/N_2003_5409.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_2003_5409.contig-group-0.log jobid: 1384 benchmark: benchmarks/gatk/haplotypecaller/N_2003_5409.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_2003_5409.bam.bai wildcards: sample=N_2003_5409, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T185.contig-group-19.g.vcf.gz, called/T185.contig-group-19.g.vcf.gz.tbi, called/T185.contig-group-19.g.done log: logs/gatk/haplotypecaller/T185.contig-group-19.log jobid: 3310 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-19.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_6928.contig-group-21.g.vcf.gz, called/N_6928.contig-group-21.g.vcf.gz.tbi, called/N_6928.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-21.log jobid: 3479 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T79.contig-group-8.g.vcf.gz, called/T79.contig-group-8.g.vcf.gz.tbi, called/T79.contig-group-8.g.done log: logs/gatk/haplotypecaller/T79.contig-group-8.log jobid: 2267 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-8.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_83.contig-group-1.g.vcf.gz, called/N_83.contig-group-1.g.vcf.gz.tbi, called/N_83.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-1.log jobid: 1567 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/N_689.contig-group-17.g.vcf.gz, called/N_689.contig-group-17.g.vcf.gz.tbi, called/N_689.contig-group-17.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-17.log jobid: 3092 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-17.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1386.bam, dedup/N_1386.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_1386.contig-group-6.g.vcf.gz, called/N_1386.contig-group-6.g.vcf.gz.tbi, called/N_1386.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_1386.contig-group-6.log jobid: 1998 benchmark: benchmarks/gatk/haplotypecaller/N_1386.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_1386.bam.bai wildcards: sample=N_1386, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1354.contig-group-9.g.vcf.gz, called/N_1354.contig-group-9.g.vcf.gz.tbi, called/N_1354.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-9.log jobid: 2283 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T180.contig-group-1.g.vcf.gz, called/T180.contig-group-1.g.vcf.gz.tbi, called/T180.contig-group-1.g.done log: logs/gatk/haplotypecaller/T180.contig-group-1.log jobid: 1580 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-1.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_6489.contig-group-16.g.vcf.gz, called/N_6489.contig-group-16.g.vcf.gz.tbi, called/N_6489.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-16.log jobid: 2993 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/T196.contig-group-22.g.vcf.gz, called/T196.contig-group-22.g.vcf.gz.tbi, called/T196.contig-group-22.g.done log: logs/gatk/haplotypecaller/T196.contig-group-22.log jobid: 3607 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-22.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N_8171.contig-group-3.g.vcf.gz, called/N_8171.contig-group-3.g.vcf.gz.tbi, called/N_8171.contig-group-3.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-3.log jobid: 1758 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-3.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_1609.contig-group-22.g.vcf.gz, called/N_1609.contig-group-22.g.vcf.gz.tbi, called/N_1609.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-22.log jobid: 3540 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1156.bam, dedup/N_1156.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_1156.contig-group-21.g.vcf.gz, called/N_1156.contig-group-21.g.vcf.gz.tbi, called/N_1156.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_1156.contig-group-21.log jobid: 3430 benchmark: benchmarks/gatk/haplotypecaller/N_1156.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_1156.bam.bai wildcards: sample=N_1156, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_689.bam, dedup/N_689.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-20.bed output: called/N_689.contig-group-20.g.vcf.gz, called/N_689.contig-group-20.g.vcf.gz.tbi, called/N_689.contig-group-20.g.done log: logs/gatk/haplotypecaller/N_689.contig-group-20.log jobid: 3380 benchmark: benchmarks/gatk/haplotypecaller/N_689.contig-group-20.bench.log reason: Input files updated by another job: dedup/N_689.bam.bai wildcards: sample=N_689, contig=contig-group-20 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T79.bam, dedup/T79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/T79.contig-group-19.g.vcf.gz, called/T79.contig-group-19.g.vcf.gz.tbi, called/T79.contig-group-19.g.done log: logs/gatk/haplotypecaller/T79.contig-group-19.log jobid: 3323 benchmark: benchmarks/gatk/haplotypecaller/T79.contig-group-19.bench.log reason: Input files updated by another job: dedup/T79.bam.bai wildcards: sample=T79, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-0.bed output: called/N_1158.contig-group-0.g.vcf.gz, called/N_1158.contig-group-0.g.vcf.gz.tbi, called/N_1158.contig-group-0.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-0.log jobid: 1332 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-0.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-0 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T1483.bam, dedup/T1483.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/T1483.contig-group-10.g.vcf.gz, called/T1483.contig-group-10.g.vcf.gz.tbi, called/T1483.contig-group-10.g.done log: logs/gatk/haplotypecaller/T1483.contig-group-10.log jobid: 2441 benchmark: benchmarks/gatk/haplotypecaller/T1483.contig-group-10.bench.log reason: Input files updated by another job: dedup/T1483.bam.bai wildcards: sample=T1483, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/T190.contig-group-14.g.vcf.gz, called/T190.contig-group-14.g.vcf.gz.tbi, called/T190.contig-group-14.g.done log: logs/gatk/haplotypecaller/T190.contig-group-14.log jobid: 2835 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-14.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-15.bed output: called/T192.contig-group-15.g.vcf.gz, called/T192.contig-group-15.g.vcf.gz.tbi, called/T192.contig-group-15.g.done log: logs/gatk/haplotypecaller/T192.contig-group-15.log jobid: 2932 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-15.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-15 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_351.bam, dedup/N_351.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-16.bed output: called/N_351.contig-group-16.g.vcf.gz, called/N_351.contig-group-16.g.vcf.gz.tbi, called/N_351.contig-group-16.g.done log: logs/gatk/haplotypecaller/N_351.contig-group-16.log jobid: 2982 benchmark: benchmarks/gatk/haplotypecaller/N_351.contig-group-16.bench.log reason: Input files updated by another job: dedup/N_351.bam.bai wildcards: sample=N_351, contig=contig-group-16 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_4843.contig-group-11.g.vcf.gz, called/N_4843.contig-group-11.g.vcf.gz.tbi, called/N_4843.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-11.log jobid: 2506 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6490.bam, dedup/N_6490.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_6490.contig-group-22.g.vcf.gz, called/N_6490.contig-group-22.g.vcf.gz.tbi, called/N_6490.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_6490.contig-group-22.log jobid: 3570 benchmark: benchmarks/gatk/haplotypecaller/N_6490.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_6490.bam.bai wildcards: sample=N_6490, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_6489.contig-group-9.g.vcf.gz, called/N_6489.contig-group-9.g.vcf.gz.tbi, called/N_6489.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-9.log jobid: 2321 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-13.bed output: called/T196.contig-group-13.g.vcf.gz, called/T196.contig-group-13.g.vcf.gz.tbi, called/T196.contig-group-13.g.done log: logs/gatk/haplotypecaller/T196.contig-group-13.log jobid: 2743 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-13.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-13 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1354.contig-group-12.g.vcf.gz, called/N_1354.contig-group-12.g.vcf.gz.tbi, called/N_1354.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-12.log jobid: 2571 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N2005.contig-group-11.g.vcf.gz, called/N2005.contig-group-11.g.vcf.gz.tbi, called/N2005.contig-group-11.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-11.log jobid: 2467 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-11.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_102.bam, dedup/N_102.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-6.bed output: called/N_102.contig-group-6.g.vcf.gz, called/N_102.contig-group-6.g.vcf.gz.tbi, called/N_102.contig-group-6.g.done log: logs/gatk/haplotypecaller/N_102.contig-group-6.log jobid: 1988 benchmark: benchmarks/gatk/haplotypecaller/N_102.contig-group-6.bench.log reason: Input files updated by another job: dedup/N_102.bam.bai wildcards: sample=N_102, contig=contig-group-6 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4847.bam, dedup/N_4847.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-21.bed output: called/N_4847.contig-group-21.g.vcf.gz, called/N_4847.contig-group-21.g.vcf.gz.tbi, called/N_4847.contig-group-21.g.done log: logs/gatk/haplotypecaller/N_4847.contig-group-21.log jobid: 3469 benchmark: benchmarks/gatk/haplotypecaller/N_4847.contig-group-21.bench.log reason: Input files updated by another job: dedup/N_4847.bam.bai wildcards: sample=N_4847, contig=contig-group-21 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_83.bam, dedup/N_83.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_83.contig-group-9.g.vcf.gz, called/N_83.contig-group-9.g.vcf.gz.tbi, called/N_83.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_83.contig-group-9.log jobid: 2335 benchmark: benchmarks/gatk/haplotypecaller/N_83.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_83.bam.bai wildcards: sample=N_83, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_1158.contig-group-18.g.vcf.gz, called/N_1158.contig-group-18.g.vcf.gz.tbi, called/N_1158.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-18.log jobid: 3144 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_1158.contig-group-12.g.vcf.gz, called/N_1158.contig-group-12.g.vcf.gz.tbi, called/N_1158.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-12.log jobid: 2568 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_79.contig-group-14.g.vcf.gz, called/N_79.contig-group-14.g.vcf.gz.tbi, called/N_79.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-14.log jobid: 2811 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8565.bam, dedup/N_8565.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-14.bed output: called/N_8565.contig-group-14.g.vcf.gz, called/N_8565.contig-group-14.g.vcf.gz.tbi, called/N_8565.contig-group-14.g.done log: logs/gatk/haplotypecaller/N_8565.contig-group-14.log jobid: 2817 benchmark: benchmarks/gatk/haplotypecaller/N_8565.contig-group-14.bench.log reason: Input files updated by another job: dedup/N_8565.bam.bai wildcards: sample=N_8565, contig=contig-group-14 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T187.bam, dedup/T187.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-8.bed output: called/T187.contig-group-8.g.vcf.gz, called/T187.contig-group-8.g.vcf.gz.tbi, called/T187.contig-group-8.g.done log: logs/gatk/haplotypecaller/T187.contig-group-8.log jobid: 2256 benchmark: benchmarks/gatk/haplotypecaller/T187.contig-group-8.bench.log reason: Input files updated by another job: dedup/T187.bam.bai wildcards: sample=T187, contig=contig-group-8 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-22.bed output: called/N_690.contig-group-22.g.vcf.gz, called/N_690.contig-group-22.g.vcf.gz.tbi, called/N_690.contig-group-22.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-22.log jobid: 3573 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-22.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-22 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_79.bam, dedup/N_79.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-2.bed output: called/N_79.contig-group-2.g.vcf.gz, called/N_79.contig-group-2.g.vcf.gz.tbi, called/N_79.contig-group-2.g.done log: logs/gatk/haplotypecaller/N_79.contig-group-2.log jobid: 1659 benchmark: benchmarks/gatk/haplotypecaller/N_79.contig-group-2.bench.log reason: Input files updated by another job: dedup/N_79.bam.bai wildcards: sample=N_79, contig=contig-group-2 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6489.bam, dedup/N_6489.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/N_6489.contig-group-18.g.vcf.gz, called/N_6489.contig-group-18.g.vcf.gz.tbi, called/N_6489.contig-group-18.g.done log: logs/gatk/haplotypecaller/N_6489.contig-group-18.log jobid: 3185 benchmark: benchmarks/gatk/haplotypecaller/N_6489.contig-group-18.bench.log reason: Input files updated by another job: dedup/N_6489.bam.bai wildcards: sample=N_6489, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_1158.contig-group-5.g.vcf.gz, called/N_1158.contig-group-5.g.vcf.gz.tbi, called/N_1158.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-5.log jobid: 1896 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9104.bam, dedup/N_9104.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_9104.contig-group-1.g.vcf.gz, called/N_9104.contig-group-1.g.vcf.gz.tbi, called/N_9104.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_9104.contig-group-1.log jobid: 1573 benchmark: benchmarks/gatk/haplotypecaller/N_9104.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_9104.bam.bai wildcards: sample=N_9104, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1157.bam, dedup/N_1157.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N_1157.contig-group-9.g.vcf.gz, called/N_1157.contig-group-9.g.vcf.gz.tbi, called/N_1157.contig-group-9.g.done log: logs/gatk/haplotypecaller/N_1157.contig-group-9.log jobid: 2279 benchmark: benchmarks/gatk/haplotypecaller/N_1157.contig-group-9.bench.log reason: Input files updated by another job: dedup/N_1157.bam.bai wildcards: sample=N_1157, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/N2005.contig-group-9.g.vcf.gz, called/N2005.contig-group-9.g.vcf.gz.tbi, called/N2005.contig-group-9.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-9.log jobid: 2275 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-9.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-12.bed output: called/N_690.contig-group-12.g.vcf.gz, called/N_690.contig-group-12.g.vcf.gz.tbi, called/N_690.contig-group-12.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-12.log jobid: 2613 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-12.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-12 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N2005.contig-group-26.g.vcf.gz, called/N2005.contig-group-26.g.vcf.gz.tbi, called/N2005.contig-group-26.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-26.log jobid: 3907 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-26.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_4843.bam, dedup/N_4843.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_4843.contig-group-5.g.vcf.gz, called/N_4843.contig-group-5.g.vcf.gz.tbi, called/N_4843.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_4843.contig-group-5.log jobid: 1930 benchmark: benchmarks/gatk/haplotypecaller/N_4843.contig-group-5.bench.log reason: Missing output files: called/N_4843.contig-group-5.g.vcf.gz, called/N_4843.contig-group-5.g.vcf.gz.tbi; Updated input files: contig-groups/contig-group-5.bed, dedup/N_4843.bam; Input files updated by another job: dedup/N_4843.bam.bai wildcards: sample=N_4843, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_8171.contig-group-1.g.vcf.gz, called/N_8171.contig-group-1.g.vcf.gz.tbi, called/N_8171.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-1.log jobid: 1566 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N2005.bam, dedup/N2005.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-3.bed output: called/N2005.contig-group-3.g.vcf.gz, called/N2005.contig-group-3.g.vcf.gz.tbi, called/N2005.contig-group-3.g.done log: logs/gatk/haplotypecaller/N2005.contig-group-3.log jobid: 1699 benchmark: benchmarks/gatk/haplotypecaller/N2005.contig-group-3.bench.log reason: Input files updated by another job: dedup/N2005.bam.bai wildcards: sample=N2005, contig=contig-group-3 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-17.bed output: called/T192.contig-group-17.g.vcf.gz, called/T192.contig-group-17.g.vcf.gz.tbi, called/T192.contig-group-17.g.done log: logs/gatk/haplotypecaller/T192.contig-group-17.log jobid: 3124 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-17.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-17 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/N_6928.contig-group-25.g.vcf.gz, called/N_6928.contig-group-25.g.vcf.gz.tbi, called/N_6928.contig-group-25.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-25.log jobid: 3863 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-25.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1354.bam, dedup/N_1354.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_1354.contig-group-26.g.vcf.gz, called/N_1354.contig-group-26.g.vcf.gz.tbi, called/N_1354.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_1354.contig-group-26.log jobid: 3915 benchmark: benchmarks/gatk/haplotypecaller/N_1354.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_1354.bam.bai wildcards: sample=N_1354, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_1158.contig-group-11.g.vcf.gz, called/N_1158.contig-group-11.g.vcf.gz.tbi, called/N_1158.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-11.log jobid: 2472 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/N_9449.contig-group-1.g.vcf.gz, called/N_9449.contig-group-1.g.vcf.gz.tbi, called/N_9449.contig-group-1.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-1.log jobid: 1574 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-1.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T192.bam, dedup/T192.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-25.bed output: called/T192.contig-group-25.g.vcf.gz, called/T192.contig-group-25.g.vcf.gz.tbi, called/T192.contig-group-25.g.done log: logs/gatk/haplotypecaller/T192.contig-group-25.log jobid: 3892 benchmark: benchmarks/gatk/haplotypecaller/T192.contig-group-25.bench.log reason: Input files updated by another job: dedup/T192.bam.bai wildcards: sample=T192, contig=contig-group-25 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_690.bam, dedup/N_690.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-10.bed output: called/N_690.contig-group-10.g.vcf.gz, called/N_690.contig-group-10.g.vcf.gz.tbi, called/N_690.contig-group-10.g.done log: logs/gatk/haplotypecaller/N_690.contig-group-10.log jobid: 2421 benchmark: benchmarks/gatk/haplotypecaller/N_690.contig-group-10.bench.log reason: Input files updated by another job: dedup/N_690.bam.bai wildcards: sample=N_690, contig=contig-group-10 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1609.bam, dedup/N_1609.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-23.bed output: called/N_1609.contig-group-23.g.vcf.gz, called/N_1609.contig-group-23.g.vcf.gz.tbi, called/N_1609.contig-group-23.g.done log: logs/gatk/haplotypecaller/N_1609.contig-group-23.log jobid: 3636 benchmark: benchmarks/gatk/haplotypecaller/N_1609.contig-group-23.bench.log reason: Input files updated by another job: dedup/N_1609.bam.bai wildcards: sample=N_1609, contig=contig-group-23 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_1158.bam, dedup/N_1158.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-19.bed output: called/N_1158.contig-group-19.g.vcf.gz, called/N_1158.contig-group-19.g.vcf.gz.tbi, called/N_1158.contig-group-19.g.done log: logs/gatk/haplotypecaller/N_1158.contig-group-19.log jobid: 3240 benchmark: benchmarks/gatk/haplotypecaller/N_1158.contig-group-19.bench.log reason: Input files updated by another job: dedup/N_1158.bam.bai wildcards: sample=N_1158, contig=contig-group-19 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_9449.bam, dedup/N_9449.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-11.bed output: called/N_9449.contig-group-11.g.vcf.gz, called/N_9449.contig-group-11.g.vcf.gz.tbi, called/N_9449.contig-group-11.g.done log: logs/gatk/haplotypecaller/N_9449.contig-group-11.log jobid: 2534 benchmark: benchmarks/gatk/haplotypecaller/N_9449.contig-group-11.bench.log reason: Input files updated by another job: dedup/N_9449.bam.bai wildcards: sample=N_9449, contig=contig-group-11 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T190.bam, dedup/T190.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-1.bed output: called/T190.contig-group-1.g.vcf.gz, called/T190.contig-group-1.g.vcf.gz.tbi, called/T190.contig-group-1.g.done log: logs/gatk/haplotypecaller/T190.contig-group-1.log jobid: 1587 benchmark: benchmarks/gatk/haplotypecaller/T190.contig-group-1.bench.log reason: Input files updated by another job: dedup/T190.bam.bai wildcards: sample=T190, contig=contig-group-1 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T180.bam, dedup/T180.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-18.bed output: called/T180.contig-group-18.g.vcf.gz, called/T180.contig-group-18.g.vcf.gz.tbi, called/T180.contig-group-18.g.done log: logs/gatk/haplotypecaller/T180.contig-group-18.log jobid: 3212 benchmark: benchmarks/gatk/haplotypecaller/T180.contig-group-18.bench.log reason: Input files updated by another job: dedup/T180.bam.bai wildcards: sample=T180, contig=contig-group-18 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_5129.bam, dedup/N_5129.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_5129.contig-group-5.g.vcf.gz, called/N_5129.contig-group-5.g.vcf.gz.tbi, called/N_5129.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_5129.contig-group-5.log jobid: 1936 benchmark: benchmarks/gatk/haplotypecaller/N_5129.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_5129.bam.bai wildcards: sample=N_5129, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_6928.bam, dedup/N_6928.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-26.bed output: called/N_6928.contig-group-26.g.vcf.gz, called/N_6928.contig-group-26.g.vcf.gz.tbi, called/N_6928.contig-group-26.g.done log: logs/gatk/haplotypecaller/N_6928.contig-group-26.log jobid: 3959 benchmark: benchmarks/gatk/haplotypecaller/N_6928.contig-group-26.bench.log reason: Input files updated by another job: dedup/N_6928.bam.bai wildcards: sample=N_6928, contig=contig-group-26 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T196.bam, dedup/T196.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-7.bed output: called/T196.contig-group-7.g.vcf.gz, called/T196.contig-group-7.g.vcf.gz.tbi, called/T196.contig-group-7.g.done log: logs/gatk/haplotypecaller/T196.contig-group-7.log jobid: 2167 benchmark: benchmarks/gatk/haplotypecaller/T196.contig-group-7.bench.log reason: Input files updated by another job: dedup/T196.bam.bai wildcards: sample=T196, contig=contig-group-7 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/T185.bam, dedup/T185.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-9.bed output: called/T185.contig-group-9.g.vcf.gz, called/T185.contig-group-9.g.vcf.gz.tbi, called/T185.contig-group-9.g.done log: logs/gatk/haplotypecaller/T185.contig-group-9.log jobid: 2350 benchmark: benchmarks/gatk/haplotypecaller/T185.contig-group-9.bench.log reason: Input files updated by another job: dedup/T185.bam.bai wildcards: sample=T185, contig=contig-group-9 threads: 2 [Mon Jul 29 13:38:43 2024] group job call_variants (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule call_variants: input: dedup/N_8171.bam, dedup/N_8171.bam.bai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, contig-groups/contig-group-5.bed output: called/N_8171.contig-group-5.g.vcf.gz, called/N_8171.contig-group-5.g.vcf.gz.tbi, called/N_8171.contig-group-5.g.done log: logs/gatk/haplotypecaller/N_8171.contig-group-5.log jobid: 1950 benchmark: benchmarks/gatk/haplotypecaller/N_8171.contig-group-5.bench.log reason: Input files updated by another job: dedup/N_8171.bam.bai wildcards: sample=N_8171, contig=contig-group-5 threads: 2 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-24.g.vcf.gz, called/M1865_2.contig-group-24.g.vcf.gz, called/M5672.contig-group-24.g.vcf.gz, called/MTDC48361.contig-group-24.g.vcf.gz, called/N2005.contig-group-24.g.vcf.gz, called/N_102.contig-group-24.g.vcf.gz, called/N_1085.contig-group-24.g.vcf.gz, called/N_1156.contig-group-24.g.vcf.gz, called/N_1157.contig-group-24.g.vcf.gz, called/N_1158.contig-group-24.g.vcf.gz, called/N_1344.contig-group-24.g.vcf.gz, called/N_1347.contig-group-24.g.vcf.gz, called/N_1354.contig-group-24.g.vcf.gz, called/N_1355.contig-group-24.g.vcf.gz, called/N_1384.contig-group-24.g.vcf.gz, called/N_1386.contig-group-24.g.vcf.gz, called/N_1390.contig-group-24.g.vcf.gz, called/N_1409.contig-group-24.g.vcf.gz, called/N_1411.contig-group-24.g.vcf.gz, called/N_1413.contig-group-24.g.vcf.gz, called/N_1414.contig-group-24.g.vcf.gz, called/N_1609.contig-group-24.g.vcf.gz, called/N_1870.contig-group-24.g.vcf.gz, called/N_1901.contig-group-24.g.vcf.gz, called/N_1913.contig-group-24.g.vcf.gz, called/N_1927.contig-group-24.g.vcf.gz, called/N_192.contig-group-24.g.vcf.gz, called/N_1934_1_1_368.contig-group-24.g.vcf.gz, called/N_1934_1_1_5973.contig-group-24.g.vcf.gz, called/N_1951_13_1951.contig-group-24.g.vcf.gz, called/N_1992_0123.contig-group-24.g.vcf.gz, called/N_1998_0130.contig-group-24.g.vcf.gz, called/N_2001_0025.contig-group-24.g.vcf.gz, called/N_2001_0205.contig-group-24.g.vcf.gz, called/N_2002_0292.contig-group-24.g.vcf.gz, called/N_2003_5409.contig-group-24.g.vcf.gz, called/N_2004.contig-group-24.g.vcf.gz, called/N_2010_1759.contig-group-24.g.vcf.gz, called/N_21.contig-group-24.g.vcf.gz, called/N_351.contig-group-24.g.vcf.gz, called/N_355.contig-group-24.g.vcf.gz, called/N_401.contig-group-24.g.vcf.gz, called/N_403.contig-group-24.g.vcf.gz, called/N_4843.contig-group-24.g.vcf.gz, called/N_4844.contig-group-24.g.vcf.gz, called/N_4846.contig-group-24.g.vcf.gz, called/N_4847.contig-group-24.g.vcf.gz, called/N_5056.contig-group-24.g.vcf.gz, called/N_5057.contig-group-24.g.vcf.gz, called/N_5129.contig-group-24.g.vcf.gz, called/N_6489.contig-group-24.g.vcf.gz, called/N_6490.contig-group-24.g.vcf.gz, called/N_685.contig-group-24.g.vcf.gz, called/N_689.contig-group-24.g.vcf.gz, called/N_690.contig-group-24.g.vcf.gz, called/N_6926.contig-group-24.g.vcf.gz, called/N_6928.contig-group-24.g.vcf.gz, called/N_6932.contig-group-24.g.vcf.gz, called/N_6.contig-group-24.g.vcf.gz, called/N_7083.contig-group-24.g.vcf.gz, called/N_79.contig-group-24.g.vcf.gz, called/N_7.contig-group-24.g.vcf.gz, called/N_8105.contig-group-24.g.vcf.gz, called/N_8171.contig-group-24.g.vcf.gz, called/N_83.contig-group-24.g.vcf.gz, called/N_8564.contig-group-24.g.vcf.gz, called/N_8565.contig-group-24.g.vcf.gz, called/N_8583.contig-group-24.g.vcf.gz, called/N_8585.contig-group-24.g.vcf.gz, called/N_8586.contig-group-24.g.vcf.gz, called/N_9104.contig-group-24.g.vcf.gz, called/N_9449.contig-group-24.g.vcf.gz, called/N_94.contig-group-24.g.vcf.gz, called/T1481.contig-group-24.g.vcf.gz, called/T1483.contig-group-24.g.vcf.gz, called/T178.contig-group-24.g.vcf.gz, called/T179.contig-group-24.g.vcf.gz, called/T180.contig-group-24.g.vcf.gz, called/T181.contig-group-24.g.vcf.gz, called/T185.contig-group-24.g.vcf.gz, called/T186.contig-group-24.g.vcf.gz, called/T187.contig-group-24.g.vcf.gz, called/T188.contig-group-24.g.vcf.gz, called/T189.contig-group-24.g.vcf.gz, called/T190.contig-group-24.g.vcf.gz, called/T192.contig-group-24.g.vcf.gz, called/T193.contig-group-24.g.vcf.gz, called/T194.contig-group-24.g.vcf.gz, called/T196.contig-group-24.g.vcf.gz, called/T248.contig-group-24.g.vcf.gz, called/T37.contig-group-24.g.vcf.gz, called/T72.contig-group-24.g.vcf.gz, called/T79.contig-group-24.g.vcf.gz, called/M1864_2.contig-group-24.g.vcf.gz.tbi, called/M1865_2.contig-group-24.g.vcf.gz.tbi, called/M5672.contig-group-24.g.vcf.gz.tbi, called/MTDC48361.contig-group-24.g.vcf.gz.tbi, called/N2005.contig-group-24.g.vcf.gz.tbi, called/N_102.contig-group-24.g.vcf.gz.tbi, called/N_1085.contig-group-24.g.vcf.gz.tbi, called/N_1156.contig-group-24.g.vcf.gz.tbi, called/N_1157.contig-group-24.g.vcf.gz.tbi, called/N_1158.contig-group-24.g.vcf.gz.tbi, called/N_1344.contig-group-24.g.vcf.gz.tbi, called/N_1347.contig-group-24.g.vcf.gz.tbi, called/N_1354.contig-group-24.g.vcf.gz.tbi, called/N_1355.contig-group-24.g.vcf.gz.tbi, called/N_1384.contig-group-24.g.vcf.gz.tbi, called/N_1386.contig-group-24.g.vcf.gz.tbi, called/N_1390.contig-group-24.g.vcf.gz.tbi, called/N_1409.contig-group-24.g.vcf.gz.tbi, called/N_1411.contig-group-24.g.vcf.gz.tbi, called/N_1413.contig-group-24.g.vcf.gz.tbi, called/N_1414.contig-group-24.g.vcf.gz.tbi, called/N_1609.contig-group-24.g.vcf.gz.tbi, called/N_1870.contig-group-24.g.vcf.gz.tbi, called/N_1901.contig-group-24.g.vcf.gz.tbi, called/N_1913.contig-group-24.g.vcf.gz.tbi, called/N_1927.contig-group-24.g.vcf.gz.tbi, called/N_192.contig-group-24.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-24.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-24.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-24.g.vcf.gz.tbi, called/N_1992_0123.contig-group-24.g.vcf.gz.tbi, called/N_1998_0130.contig-group-24.g.vcf.gz.tbi, called/N_2001_0025.contig-group-24.g.vcf.gz.tbi, called/N_2001_0205.contig-group-24.g.vcf.gz.tbi, called/N_2002_0292.contig-group-24.g.vcf.gz.tbi, called/N_2003_5409.contig-group-24.g.vcf.gz.tbi, called/N_2004.contig-group-24.g.vcf.gz.tbi, called/N_2010_1759.contig-group-24.g.vcf.gz.tbi, called/N_21.contig-group-24.g.vcf.gz.tbi, called/N_351.contig-group-24.g.vcf.gz.tbi, called/N_355.contig-group-24.g.vcf.gz.tbi, called/N_401.contig-group-24.g.vcf.gz.tbi, called/N_403.contig-group-24.g.vcf.gz.tbi, called/N_4843.contig-group-24.g.vcf.gz.tbi, called/N_4844.contig-group-24.g.vcf.gz.tbi, called/N_4846.contig-group-24.g.vcf.gz.tbi, called/N_4847.contig-group-24.g.vcf.gz.tbi, called/N_5056.contig-group-24.g.vcf.gz.tbi, called/N_5057.contig-group-24.g.vcf.gz.tbi, called/N_5129.contig-group-24.g.vcf.gz.tbi, called/N_6489.contig-group-24.g.vcf.gz.tbi, called/N_6490.contig-group-24.g.vcf.gz.tbi, called/N_685.contig-group-24.g.vcf.gz.tbi, called/N_689.contig-group-24.g.vcf.gz.tbi, called/N_690.contig-group-24.g.vcf.gz.tbi, called/N_6926.contig-group-24.g.vcf.gz.tbi, called/N_6928.contig-group-24.g.vcf.gz.tbi, called/N_6932.contig-group-24.g.vcf.gz.tbi, called/N_6.contig-group-24.g.vcf.gz.tbi, called/N_7083.contig-group-24.g.vcf.gz.tbi, called/N_79.contig-group-24.g.vcf.gz.tbi, called/N_7.contig-group-24.g.vcf.gz.tbi, called/N_8105.contig-group-24.g.vcf.gz.tbi, called/N_8171.contig-group-24.g.vcf.gz.tbi, called/N_83.contig-group-24.g.vcf.gz.tbi, called/N_8564.contig-group-24.g.vcf.gz.tbi, called/N_8565.contig-group-24.g.vcf.gz.tbi, called/N_8583.contig-group-24.g.vcf.gz.tbi, called/N_8585.contig-group-24.g.vcf.gz.tbi, called/N_8586.contig-group-24.g.vcf.gz.tbi, called/N_9104.contig-group-24.g.vcf.gz.tbi, called/N_9449.contig-group-24.g.vcf.gz.tbi, called/N_94.contig-group-24.g.vcf.gz.tbi, called/T1481.contig-group-24.g.vcf.gz.tbi, called/T1483.contig-group-24.g.vcf.gz.tbi, called/T178.contig-group-24.g.vcf.gz.tbi, called/T179.contig-group-24.g.vcf.gz.tbi, called/T180.contig-group-24.g.vcf.gz.tbi, called/T181.contig-group-24.g.vcf.gz.tbi, called/T185.contig-group-24.g.vcf.gz.tbi, called/T186.contig-group-24.g.vcf.gz.tbi, called/T187.contig-group-24.g.vcf.gz.tbi, called/T188.contig-group-24.g.vcf.gz.tbi, called/T189.contig-group-24.g.vcf.gz.tbi, called/T190.contig-group-24.g.vcf.gz.tbi, called/T192.contig-group-24.g.vcf.gz.tbi, called/T193.contig-group-24.g.vcf.gz.tbi, called/T194.contig-group-24.g.vcf.gz.tbi, called/T196.contig-group-24.g.vcf.gz.tbi, called/T248.contig-group-24.g.vcf.gz.tbi, called/T37.contig-group-24.g.vcf.gz.tbi, called/T72.contig-group-24.g.vcf.gz.tbi, called/T79.contig-group-24.g.vcf.gz.tbi output: called/all.contig-group-24.g.vcf.gz, called/all.contig-group-24.g.done log: logs/gatk/combine-gvcfs/contig-group-24.log jobid: 3709 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-24.bench.log reason: Input files updated by another job: called/T185.contig-group-24.g.vcf.gz.tbi, called/N_1386.contig-group-24.g.vcf.gz, called/N_79.contig-group-24.g.vcf.gz, called/N_1156.contig-group-24.g.vcf.gz, called/N_5129.contig-group-24.g.vcf.gz.tbi, called/T1483.contig-group-24.g.vcf.gz, called/T1483.contig-group-24.g.vcf.gz.tbi, called/N_1870.contig-group-24.g.vcf.gz.tbi, called/N_6928.contig-group-24.g.vcf.gz.tbi, called/N_8171.contig-group-24.g.vcf.gz, called/N_1157.contig-group-24.g.vcf.gz, called/N_1386.contig-group-24.g.vcf.gz.tbi, called/N_1992_0123.contig-group-24.g.vcf.gz, called/N2005.contig-group-24.g.vcf.gz, called/N_6489.contig-group-24.g.vcf.gz, called/N_4843.contig-group-24.g.vcf.gz.tbi, called/N_102.contig-group-24.g.vcf.gz.tbi, called/T187.contig-group-24.g.vcf.gz.tbi, called/N_83.contig-group-24.g.vcf.gz.tbi, called/N_6928.contig-group-24.g.vcf.gz, called/T187.contig-group-24.g.vcf.gz, called/N_1870.contig-group-24.g.vcf.gz, called/T180.contig-group-24.g.vcf.gz.tbi, called/N_8565.contig-group-24.g.vcf.gz, called/N_8583.contig-group-24.g.vcf.gz.tbi, called/N_9104.contig-group-24.g.vcf.gz.tbi, called/N_351.contig-group-24.g.vcf.gz.tbi, called/N_6490.contig-group-24.g.vcf.gz.tbi, called/N_9104.contig-group-24.g.vcf.gz, called/T196.contig-group-24.g.vcf.gz.tbi, called/T180.contig-group-24.g.vcf.gz, called/T192.contig-group-24.g.vcf.gz, called/N_1354.contig-group-24.g.vcf.gz.tbi, called/N_1158.contig-group-24.g.vcf.gz, called/N_9449.contig-group-24.g.vcf.gz, called/T190.contig-group-24.g.vcf.gz.tbi, called/N_9449.contig-group-24.g.vcf.gz.tbi, called/N2005.contig-group-24.g.vcf.gz.tbi, called/N_1609.contig-group-24.g.vcf.gz.tbi, called/N_689.contig-group-24.g.vcf.gz, called/N_4847.contig-group-24.g.vcf.gz, called/N_2003_5409.contig-group-24.g.vcf.gz.tbi, called/N_1158.contig-group-24.g.vcf.gz.tbi, called/N_1156.contig-group-24.g.vcf.gz.tbi, called/N_83.contig-group-24.g.vcf.gz, called/T196.contig-group-24.g.vcf.gz, called/N_689.contig-group-24.g.vcf.gz.tbi, called/N_8171.contig-group-24.g.vcf.gz.tbi, called/N_690.contig-group-24.g.vcf.gz.tbi, called/N_8583.contig-group-24.g.vcf.gz, called/T72.contig-group-24.g.vcf.gz, called/N_6490.contig-group-24.g.vcf.gz, called/N_4847.contig-group-24.g.vcf.gz.tbi, called/N_4843.contig-group-24.g.vcf.gz, called/N_1609.contig-group-24.g.vcf.gz, called/N_351.contig-group-24.g.vcf.gz, called/M5672.contig-group-24.g.vcf.gz.tbi, called/T192.contig-group-24.g.vcf.gz.tbi, called/N_5129.contig-group-24.g.vcf.gz, called/N_1934_1_1_5973.contig-group-24.g.vcf.gz.tbi, called/N_79.contig-group-24.g.vcf.gz.tbi, called/N_1354.contig-group-24.g.vcf.gz, called/T185.contig-group-24.g.vcf.gz, called/N_1927.contig-group-24.g.vcf.gz, called/T190.contig-group-24.g.vcf.gz, called/N_6489.contig-group-24.g.vcf.gz.tbi, called/N_102.contig-group-24.g.vcf.gz, called/N_1157.contig-group-24.g.vcf.gz.tbi, called/N_8565.contig-group-24.g.vcf.gz.tbi, called/N_690.contig-group-24.g.vcf.gz, called/N_1992_0123.contig-group-24.g.vcf.gz.tbi, called/T79.contig-group-24.g.vcf.gz, called/M5672.contig-group-24.g.vcf.gz, called/T72.contig-group-24.g.vcf.gz.tbi, called/N_1927.contig-group-24.g.vcf.gz.tbi, called/N_2003_5409.contig-group-24.g.vcf.gz, called/N_1934_1_1_5973.contig-group-24.g.vcf.gz, called/T79.contig-group-24.g.vcf.gz.tbi wildcards: contig=contig-group-24 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-3.g.vcf.gz, called/M1865_2.contig-group-3.g.vcf.gz, called/M5672.contig-group-3.g.vcf.gz, called/MTDC48361.contig-group-3.g.vcf.gz, called/N2005.contig-group-3.g.vcf.gz, called/N_102.contig-group-3.g.vcf.gz, called/N_1085.contig-group-3.g.vcf.gz, called/N_1156.contig-group-3.g.vcf.gz, called/N_1157.contig-group-3.g.vcf.gz, called/N_1158.contig-group-3.g.vcf.gz, called/N_1344.contig-group-3.g.vcf.gz, called/N_1347.contig-group-3.g.vcf.gz, called/N_1354.contig-group-3.g.vcf.gz, called/N_1355.contig-group-3.g.vcf.gz, called/N_1384.contig-group-3.g.vcf.gz, called/N_1386.contig-group-3.g.vcf.gz, called/N_1390.contig-group-3.g.vcf.gz, called/N_1409.contig-group-3.g.vcf.gz, called/N_1411.contig-group-3.g.vcf.gz, called/N_1413.contig-group-3.g.vcf.gz, called/N_1414.contig-group-3.g.vcf.gz, called/N_1609.contig-group-3.g.vcf.gz, called/N_1870.contig-group-3.g.vcf.gz, called/N_1901.contig-group-3.g.vcf.gz, called/N_1913.contig-group-3.g.vcf.gz, called/N_1927.contig-group-3.g.vcf.gz, called/N_192.contig-group-3.g.vcf.gz, called/N_1934_1_1_368.contig-group-3.g.vcf.gz, called/N_1934_1_1_5973.contig-group-3.g.vcf.gz, called/N_1951_13_1951.contig-group-3.g.vcf.gz, called/N_1992_0123.contig-group-3.g.vcf.gz, called/N_1998_0130.contig-group-3.g.vcf.gz, called/N_2001_0025.contig-group-3.g.vcf.gz, called/N_2001_0205.contig-group-3.g.vcf.gz, called/N_2002_0292.contig-group-3.g.vcf.gz, called/N_2003_5409.contig-group-3.g.vcf.gz, called/N_2004.contig-group-3.g.vcf.gz, called/N_2010_1759.contig-group-3.g.vcf.gz, called/N_21.contig-group-3.g.vcf.gz, called/N_351.contig-group-3.g.vcf.gz, called/N_355.contig-group-3.g.vcf.gz, called/N_401.contig-group-3.g.vcf.gz, called/N_403.contig-group-3.g.vcf.gz, called/N_4843.contig-group-3.g.vcf.gz, called/N_4844.contig-group-3.g.vcf.gz, called/N_4846.contig-group-3.g.vcf.gz, called/N_4847.contig-group-3.g.vcf.gz, called/N_5056.contig-group-3.g.vcf.gz, called/N_5057.contig-group-3.g.vcf.gz, called/N_5129.contig-group-3.g.vcf.gz, called/N_6489.contig-group-3.g.vcf.gz, called/N_6490.contig-group-3.g.vcf.gz, called/N_685.contig-group-3.g.vcf.gz, called/N_689.contig-group-3.g.vcf.gz, called/N_690.contig-group-3.g.vcf.gz, called/N_6926.contig-group-3.g.vcf.gz, called/N_6928.contig-group-3.g.vcf.gz, called/N_6932.contig-group-3.g.vcf.gz, called/N_6.contig-group-3.g.vcf.gz, called/N_7083.contig-group-3.g.vcf.gz, called/N_79.contig-group-3.g.vcf.gz, called/N_7.contig-group-3.g.vcf.gz, called/N_8105.contig-group-3.g.vcf.gz, called/N_8171.contig-group-3.g.vcf.gz, called/N_83.contig-group-3.g.vcf.gz, called/N_8564.contig-group-3.g.vcf.gz, called/N_8565.contig-group-3.g.vcf.gz, called/N_8583.contig-group-3.g.vcf.gz, called/N_8585.contig-group-3.g.vcf.gz, called/N_8586.contig-group-3.g.vcf.gz, called/N_9104.contig-group-3.g.vcf.gz, called/N_9449.contig-group-3.g.vcf.gz, called/N_94.contig-group-3.g.vcf.gz, called/T1481.contig-group-3.g.vcf.gz, called/T1483.contig-group-3.g.vcf.gz, called/T178.contig-group-3.g.vcf.gz, called/T179.contig-group-3.g.vcf.gz, called/T180.contig-group-3.g.vcf.gz, called/T181.contig-group-3.g.vcf.gz, called/T185.contig-group-3.g.vcf.gz, called/T186.contig-group-3.g.vcf.gz, called/T187.contig-group-3.g.vcf.gz, called/T188.contig-group-3.g.vcf.gz, called/T189.contig-group-3.g.vcf.gz, called/T190.contig-group-3.g.vcf.gz, called/T192.contig-group-3.g.vcf.gz, called/T193.contig-group-3.g.vcf.gz, called/T194.contig-group-3.g.vcf.gz, called/T196.contig-group-3.g.vcf.gz, called/T248.contig-group-3.g.vcf.gz, called/T37.contig-group-3.g.vcf.gz, called/T72.contig-group-3.g.vcf.gz, called/T79.contig-group-3.g.vcf.gz, called/M1864_2.contig-group-3.g.vcf.gz.tbi, called/M1865_2.contig-group-3.g.vcf.gz.tbi, called/M5672.contig-group-3.g.vcf.gz.tbi, called/MTDC48361.contig-group-3.g.vcf.gz.tbi, called/N2005.contig-group-3.g.vcf.gz.tbi, called/N_102.contig-group-3.g.vcf.gz.tbi, called/N_1085.contig-group-3.g.vcf.gz.tbi, called/N_1156.contig-group-3.g.vcf.gz.tbi, called/N_1157.contig-group-3.g.vcf.gz.tbi, called/N_1158.contig-group-3.g.vcf.gz.tbi, called/N_1344.contig-group-3.g.vcf.gz.tbi, called/N_1347.contig-group-3.g.vcf.gz.tbi, called/N_1354.contig-group-3.g.vcf.gz.tbi, called/N_1355.contig-group-3.g.vcf.gz.tbi, called/N_1384.contig-group-3.g.vcf.gz.tbi, called/N_1386.contig-group-3.g.vcf.gz.tbi, called/N_1390.contig-group-3.g.vcf.gz.tbi, called/N_1409.contig-group-3.g.vcf.gz.tbi, called/N_1411.contig-group-3.g.vcf.gz.tbi, called/N_1413.contig-group-3.g.vcf.gz.tbi, called/N_1414.contig-group-3.g.vcf.gz.tbi, called/N_1609.contig-group-3.g.vcf.gz.tbi, called/N_1870.contig-group-3.g.vcf.gz.tbi, called/N_1901.contig-group-3.g.vcf.gz.tbi, called/N_1913.contig-group-3.g.vcf.gz.tbi, called/N_1927.contig-group-3.g.vcf.gz.tbi, called/N_192.contig-group-3.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-3.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-3.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-3.g.vcf.gz.tbi, called/N_1992_0123.contig-group-3.g.vcf.gz.tbi, called/N_1998_0130.contig-group-3.g.vcf.gz.tbi, called/N_2001_0025.contig-group-3.g.vcf.gz.tbi, called/N_2001_0205.contig-group-3.g.vcf.gz.tbi, called/N_2002_0292.contig-group-3.g.vcf.gz.tbi, called/N_2003_5409.contig-group-3.g.vcf.gz.tbi, called/N_2004.contig-group-3.g.vcf.gz.tbi, called/N_2010_1759.contig-group-3.g.vcf.gz.tbi, called/N_21.contig-group-3.g.vcf.gz.tbi, called/N_351.contig-group-3.g.vcf.gz.tbi, called/N_355.contig-group-3.g.vcf.gz.tbi, called/N_401.contig-group-3.g.vcf.gz.tbi, called/N_403.contig-group-3.g.vcf.gz.tbi, called/N_4843.contig-group-3.g.vcf.gz.tbi, called/N_4844.contig-group-3.g.vcf.gz.tbi, called/N_4846.contig-group-3.g.vcf.gz.tbi, called/N_4847.contig-group-3.g.vcf.gz.tbi, called/N_5056.contig-group-3.g.vcf.gz.tbi, called/N_5057.contig-group-3.g.vcf.gz.tbi, called/N_5129.contig-group-3.g.vcf.gz.tbi, called/N_6489.contig-group-3.g.vcf.gz.tbi, called/N_6490.contig-group-3.g.vcf.gz.tbi, called/N_685.contig-group-3.g.vcf.gz.tbi, called/N_689.contig-group-3.g.vcf.gz.tbi, called/N_690.contig-group-3.g.vcf.gz.tbi, called/N_6926.contig-group-3.g.vcf.gz.tbi, called/N_6928.contig-group-3.g.vcf.gz.tbi, called/N_6932.contig-group-3.g.vcf.gz.tbi, called/N_6.contig-group-3.g.vcf.gz.tbi, called/N_7083.contig-group-3.g.vcf.gz.tbi, called/N_79.contig-group-3.g.vcf.gz.tbi, called/N_7.contig-group-3.g.vcf.gz.tbi, called/N_8105.contig-group-3.g.vcf.gz.tbi, called/N_8171.contig-group-3.g.vcf.gz.tbi, called/N_83.contig-group-3.g.vcf.gz.tbi, called/N_8564.contig-group-3.g.vcf.gz.tbi, called/N_8565.contig-group-3.g.vcf.gz.tbi, called/N_8583.contig-group-3.g.vcf.gz.tbi, called/N_8585.contig-group-3.g.vcf.gz.tbi, called/N_8586.contig-group-3.g.vcf.gz.tbi, called/N_9104.contig-group-3.g.vcf.gz.tbi, called/N_9449.contig-group-3.g.vcf.gz.tbi, called/N_94.contig-group-3.g.vcf.gz.tbi, called/T1481.contig-group-3.g.vcf.gz.tbi, called/T1483.contig-group-3.g.vcf.gz.tbi, called/T178.contig-group-3.g.vcf.gz.tbi, called/T179.contig-group-3.g.vcf.gz.tbi, called/T180.contig-group-3.g.vcf.gz.tbi, called/T181.contig-group-3.g.vcf.gz.tbi, called/T185.contig-group-3.g.vcf.gz.tbi, called/T186.contig-group-3.g.vcf.gz.tbi, called/T187.contig-group-3.g.vcf.gz.tbi, called/T188.contig-group-3.g.vcf.gz.tbi, called/T189.contig-group-3.g.vcf.gz.tbi, called/T190.contig-group-3.g.vcf.gz.tbi, called/T192.contig-group-3.g.vcf.gz.tbi, called/T193.contig-group-3.g.vcf.gz.tbi, called/T194.contig-group-3.g.vcf.gz.tbi, called/T196.contig-group-3.g.vcf.gz.tbi, called/T248.contig-group-3.g.vcf.gz.tbi, called/T37.contig-group-3.g.vcf.gz.tbi, called/T72.contig-group-3.g.vcf.gz.tbi, called/T79.contig-group-3.g.vcf.gz.tbi output: called/all.contig-group-3.g.vcf.gz, called/all.contig-group-3.g.done log: logs/gatk/combine-gvcfs/contig-group-3.log jobid: 1693 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-3.bench.log reason: Input files updated by another job: called/T79.contig-group-3.g.vcf.gz, called/N_1157.contig-group-3.g.vcf.gz.tbi, called/N_8583.contig-group-3.g.vcf.gz.tbi, called/N_6490.contig-group-3.g.vcf.gz, called/T185.contig-group-3.g.vcf.gz.tbi, called/N_351.contig-group-3.g.vcf.gz.tbi, called/N_5129.contig-group-3.g.vcf.gz.tbi, called/N_1870.contig-group-3.g.vcf.gz, called/N_8171.contig-group-3.g.vcf.gz.tbi, called/T196.contig-group-3.g.vcf.gz.tbi, called/T1483.contig-group-3.g.vcf.gz.tbi, called/N_2003_5409.contig-group-3.g.vcf.gz, called/N_4843.contig-group-3.g.vcf.gz.tbi, called/N_1609.contig-group-3.g.vcf.gz, called/N_1934_1_1_5973.contig-group-3.g.vcf.gz.tbi, called/N_1927.contig-group-3.g.vcf.gz, called/N_1157.contig-group-3.g.vcf.gz, called/N_689.contig-group-3.g.vcf.gz, called/N_351.contig-group-3.g.vcf.gz, called/N_8583.contig-group-3.g.vcf.gz, called/N_1609.contig-group-3.g.vcf.gz.tbi, called/N_1386.contig-group-3.g.vcf.gz, called/M5672.contig-group-3.g.vcf.gz, called/T72.contig-group-3.g.vcf.gz, called/T190.contig-group-3.g.vcf.gz, called/N_690.contig-group-3.g.vcf.gz, called/N_102.contig-group-3.g.vcf.gz, called/T192.contig-group-3.g.vcf.gz, called/N_9104.contig-group-3.g.vcf.gz.tbi, called/N_1158.contig-group-3.g.vcf.gz, called/N_4847.contig-group-3.g.vcf.gz, called/T72.contig-group-3.g.vcf.gz.tbi, called/N_4843.contig-group-3.g.vcf.gz, called/N_9449.contig-group-3.g.vcf.gz, called/N_83.contig-group-3.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-3.g.vcf.gz, called/N_690.contig-group-3.g.vcf.gz.tbi, called/N_8565.contig-group-3.g.vcf.gz.tbi, called/N_9104.contig-group-3.g.vcf.gz, called/N_102.contig-group-3.g.vcf.gz.tbi, called/T187.contig-group-3.g.vcf.gz.tbi, called/N_1927.contig-group-3.g.vcf.gz.tbi, called/N_8171.contig-group-3.g.vcf.gz, called/T180.contig-group-3.g.vcf.gz, called/T1483.contig-group-3.g.vcf.gz, called/N_1156.contig-group-3.g.vcf.gz, called/T192.contig-group-3.g.vcf.gz.tbi, called/N_1156.contig-group-3.g.vcf.gz.tbi, called/T79.contig-group-3.g.vcf.gz.tbi, called/N_79.contig-group-3.g.vcf.gz, called/N_1992_0123.contig-group-3.g.vcf.gz, called/N_83.contig-group-3.g.vcf.gz, called/N_6928.contig-group-3.g.vcf.gz.tbi, called/N_79.contig-group-3.g.vcf.gz.tbi, called/T180.contig-group-3.g.vcf.gz.tbi, called/N_1158.contig-group-3.g.vcf.gz.tbi, called/N_1386.contig-group-3.g.vcf.gz.tbi, called/N_6489.contig-group-3.g.vcf.gz, called/N_6489.contig-group-3.g.vcf.gz.tbi, called/N_1992_0123.contig-group-3.g.vcf.gz.tbi, called/N_1354.contig-group-3.g.vcf.gz.tbi, called/N_4847.contig-group-3.g.vcf.gz.tbi, called/N_1870.contig-group-3.g.vcf.gz.tbi, called/M5672.contig-group-3.g.vcf.gz.tbi, called/N_5129.contig-group-3.g.vcf.gz, called/N_1354.contig-group-3.g.vcf.gz, called/N2005.contig-group-3.g.vcf.gz, called/N_8565.contig-group-3.g.vcf.gz, called/T190.contig-group-3.g.vcf.gz.tbi, called/N2005.contig-group-3.g.vcf.gz.tbi, called/T185.contig-group-3.g.vcf.gz, called/N_6928.contig-group-3.g.vcf.gz, called/N_689.contig-group-3.g.vcf.gz.tbi, called/N_9449.contig-group-3.g.vcf.gz.tbi, called/N_6490.contig-group-3.g.vcf.gz.tbi, called/T196.contig-group-3.g.vcf.gz, called/N_2003_5409.contig-group-3.g.vcf.gz.tbi, called/T187.contig-group-3.g.vcf.gz wildcards: contig=contig-group-3 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-17.g.vcf.gz, called/M1865_2.contig-group-17.g.vcf.gz, called/M5672.contig-group-17.g.vcf.gz, called/MTDC48361.contig-group-17.g.vcf.gz, called/N2005.contig-group-17.g.vcf.gz, called/N_102.contig-group-17.g.vcf.gz, called/N_1085.contig-group-17.g.vcf.gz, called/N_1156.contig-group-17.g.vcf.gz, called/N_1157.contig-group-17.g.vcf.gz, called/N_1158.contig-group-17.g.vcf.gz, called/N_1344.contig-group-17.g.vcf.gz, called/N_1347.contig-group-17.g.vcf.gz, called/N_1354.contig-group-17.g.vcf.gz, called/N_1355.contig-group-17.g.vcf.gz, called/N_1384.contig-group-17.g.vcf.gz, called/N_1386.contig-group-17.g.vcf.gz, called/N_1390.contig-group-17.g.vcf.gz, called/N_1409.contig-group-17.g.vcf.gz, called/N_1411.contig-group-17.g.vcf.gz, called/N_1413.contig-group-17.g.vcf.gz, called/N_1414.contig-group-17.g.vcf.gz, called/N_1609.contig-group-17.g.vcf.gz, called/N_1870.contig-group-17.g.vcf.gz, called/N_1901.contig-group-17.g.vcf.gz, called/N_1913.contig-group-17.g.vcf.gz, called/N_1927.contig-group-17.g.vcf.gz, called/N_192.contig-group-17.g.vcf.gz, called/N_1934_1_1_368.contig-group-17.g.vcf.gz, called/N_1934_1_1_5973.contig-group-17.g.vcf.gz, called/N_1951_13_1951.contig-group-17.g.vcf.gz, called/N_1992_0123.contig-group-17.g.vcf.gz, called/N_1998_0130.contig-group-17.g.vcf.gz, called/N_2001_0025.contig-group-17.g.vcf.gz, called/N_2001_0205.contig-group-17.g.vcf.gz, called/N_2002_0292.contig-group-17.g.vcf.gz, called/N_2003_5409.contig-group-17.g.vcf.gz, called/N_2004.contig-group-17.g.vcf.gz, called/N_2010_1759.contig-group-17.g.vcf.gz, called/N_21.contig-group-17.g.vcf.gz, called/N_351.contig-group-17.g.vcf.gz, called/N_355.contig-group-17.g.vcf.gz, called/N_401.contig-group-17.g.vcf.gz, called/N_403.contig-group-17.g.vcf.gz, called/N_4843.contig-group-17.g.vcf.gz, called/N_4844.contig-group-17.g.vcf.gz, called/N_4846.contig-group-17.g.vcf.gz, called/N_4847.contig-group-17.g.vcf.gz, called/N_5056.contig-group-17.g.vcf.gz, called/N_5057.contig-group-17.g.vcf.gz, called/N_5129.contig-group-17.g.vcf.gz, called/N_6489.contig-group-17.g.vcf.gz, called/N_6490.contig-group-17.g.vcf.gz, called/N_685.contig-group-17.g.vcf.gz, called/N_689.contig-group-17.g.vcf.gz, called/N_690.contig-group-17.g.vcf.gz, called/N_6926.contig-group-17.g.vcf.gz, called/N_6928.contig-group-17.g.vcf.gz, called/N_6932.contig-group-17.g.vcf.gz, called/N_6.contig-group-17.g.vcf.gz, called/N_7083.contig-group-17.g.vcf.gz, called/N_79.contig-group-17.g.vcf.gz, called/N_7.contig-group-17.g.vcf.gz, called/N_8105.contig-group-17.g.vcf.gz, called/N_8171.contig-group-17.g.vcf.gz, called/N_83.contig-group-17.g.vcf.gz, called/N_8564.contig-group-17.g.vcf.gz, called/N_8565.contig-group-17.g.vcf.gz, called/N_8583.contig-group-17.g.vcf.gz, called/N_8585.contig-group-17.g.vcf.gz, called/N_8586.contig-group-17.g.vcf.gz, called/N_9104.contig-group-17.g.vcf.gz, called/N_9449.contig-group-17.g.vcf.gz, called/N_94.contig-group-17.g.vcf.gz, called/T1481.contig-group-17.g.vcf.gz, called/T1483.contig-group-17.g.vcf.gz, called/T178.contig-group-17.g.vcf.gz, called/T179.contig-group-17.g.vcf.gz, called/T180.contig-group-17.g.vcf.gz, called/T181.contig-group-17.g.vcf.gz, called/T185.contig-group-17.g.vcf.gz, called/T186.contig-group-17.g.vcf.gz, called/T187.contig-group-17.g.vcf.gz, called/T188.contig-group-17.g.vcf.gz, called/T189.contig-group-17.g.vcf.gz, called/T190.contig-group-17.g.vcf.gz, called/T192.contig-group-17.g.vcf.gz, called/T193.contig-group-17.g.vcf.gz, called/T194.contig-group-17.g.vcf.gz, called/T196.contig-group-17.g.vcf.gz, called/T248.contig-group-17.g.vcf.gz, called/T37.contig-group-17.g.vcf.gz, called/T72.contig-group-17.g.vcf.gz, called/T79.contig-group-17.g.vcf.gz, called/M1864_2.contig-group-17.g.vcf.gz.tbi, called/M1865_2.contig-group-17.g.vcf.gz.tbi, called/M5672.contig-group-17.g.vcf.gz.tbi, called/MTDC48361.contig-group-17.g.vcf.gz.tbi, called/N2005.contig-group-17.g.vcf.gz.tbi, called/N_102.contig-group-17.g.vcf.gz.tbi, called/N_1085.contig-group-17.g.vcf.gz.tbi, called/N_1156.contig-group-17.g.vcf.gz.tbi, called/N_1157.contig-group-17.g.vcf.gz.tbi, called/N_1158.contig-group-17.g.vcf.gz.tbi, called/N_1344.contig-group-17.g.vcf.gz.tbi, called/N_1347.contig-group-17.g.vcf.gz.tbi, called/N_1354.contig-group-17.g.vcf.gz.tbi, called/N_1355.contig-group-17.g.vcf.gz.tbi, called/N_1384.contig-group-17.g.vcf.gz.tbi, called/N_1386.contig-group-17.g.vcf.gz.tbi, called/N_1390.contig-group-17.g.vcf.gz.tbi, called/N_1409.contig-group-17.g.vcf.gz.tbi, called/N_1411.contig-group-17.g.vcf.gz.tbi, called/N_1413.contig-group-17.g.vcf.gz.tbi, called/N_1414.contig-group-17.g.vcf.gz.tbi, called/N_1609.contig-group-17.g.vcf.gz.tbi, called/N_1870.contig-group-17.g.vcf.gz.tbi, called/N_1901.contig-group-17.g.vcf.gz.tbi, called/N_1913.contig-group-17.g.vcf.gz.tbi, called/N_1927.contig-group-17.g.vcf.gz.tbi, called/N_192.contig-group-17.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-17.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-17.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-17.g.vcf.gz.tbi, called/N_1992_0123.contig-group-17.g.vcf.gz.tbi, called/N_1998_0130.contig-group-17.g.vcf.gz.tbi, called/N_2001_0025.contig-group-17.g.vcf.gz.tbi, called/N_2001_0205.contig-group-17.g.vcf.gz.tbi, called/N_2002_0292.contig-group-17.g.vcf.gz.tbi, called/N_2003_5409.contig-group-17.g.vcf.gz.tbi, called/N_2004.contig-group-17.g.vcf.gz.tbi, called/N_2010_1759.contig-group-17.g.vcf.gz.tbi, called/N_21.contig-group-17.g.vcf.gz.tbi, called/N_351.contig-group-17.g.vcf.gz.tbi, called/N_355.contig-group-17.g.vcf.gz.tbi, called/N_401.contig-group-17.g.vcf.gz.tbi, called/N_403.contig-group-17.g.vcf.gz.tbi, called/N_4843.contig-group-17.g.vcf.gz.tbi, called/N_4844.contig-group-17.g.vcf.gz.tbi, called/N_4846.contig-group-17.g.vcf.gz.tbi, called/N_4847.contig-group-17.g.vcf.gz.tbi, called/N_5056.contig-group-17.g.vcf.gz.tbi, called/N_5057.contig-group-17.g.vcf.gz.tbi, called/N_5129.contig-group-17.g.vcf.gz.tbi, called/N_6489.contig-group-17.g.vcf.gz.tbi, called/N_6490.contig-group-17.g.vcf.gz.tbi, called/N_685.contig-group-17.g.vcf.gz.tbi, called/N_689.contig-group-17.g.vcf.gz.tbi, called/N_690.contig-group-17.g.vcf.gz.tbi, called/N_6926.contig-group-17.g.vcf.gz.tbi, called/N_6928.contig-group-17.g.vcf.gz.tbi, called/N_6932.contig-group-17.g.vcf.gz.tbi, called/N_6.contig-group-17.g.vcf.gz.tbi, called/N_7083.contig-group-17.g.vcf.gz.tbi, called/N_79.contig-group-17.g.vcf.gz.tbi, called/N_7.contig-group-17.g.vcf.gz.tbi, called/N_8105.contig-group-17.g.vcf.gz.tbi, called/N_8171.contig-group-17.g.vcf.gz.tbi, called/N_83.contig-group-17.g.vcf.gz.tbi, called/N_8564.contig-group-17.g.vcf.gz.tbi, called/N_8565.contig-group-17.g.vcf.gz.tbi, called/N_8583.contig-group-17.g.vcf.gz.tbi, called/N_8585.contig-group-17.g.vcf.gz.tbi, called/N_8586.contig-group-17.g.vcf.gz.tbi, called/N_9104.contig-group-17.g.vcf.gz.tbi, called/N_9449.contig-group-17.g.vcf.gz.tbi, called/N_94.contig-group-17.g.vcf.gz.tbi, called/T1481.contig-group-17.g.vcf.gz.tbi, called/T1483.contig-group-17.g.vcf.gz.tbi, called/T178.contig-group-17.g.vcf.gz.tbi, called/T179.contig-group-17.g.vcf.gz.tbi, called/T180.contig-group-17.g.vcf.gz.tbi, called/T181.contig-group-17.g.vcf.gz.tbi, called/T185.contig-group-17.g.vcf.gz.tbi, called/T186.contig-group-17.g.vcf.gz.tbi, called/T187.contig-group-17.g.vcf.gz.tbi, called/T188.contig-group-17.g.vcf.gz.tbi, called/T189.contig-group-17.g.vcf.gz.tbi, called/T190.contig-group-17.g.vcf.gz.tbi, called/T192.contig-group-17.g.vcf.gz.tbi, called/T193.contig-group-17.g.vcf.gz.tbi, called/T194.contig-group-17.g.vcf.gz.tbi, called/T196.contig-group-17.g.vcf.gz.tbi, called/T248.contig-group-17.g.vcf.gz.tbi, called/T37.contig-group-17.g.vcf.gz.tbi, called/T72.contig-group-17.g.vcf.gz.tbi, called/T79.contig-group-17.g.vcf.gz.tbi output: called/all.contig-group-17.g.vcf.gz, called/all.contig-group-17.g.done log: logs/gatk/combine-gvcfs/contig-group-17.log jobid: 3037 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-17.bench.log reason: Input files updated by another job: called/N_1870.contig-group-17.g.vcf.gz.tbi, called/N2005.contig-group-17.g.vcf.gz, called/N_1158.contig-group-17.g.vcf.gz.tbi, called/N_1870.contig-group-17.g.vcf.gz, called/N_1992_0123.contig-group-17.g.vcf.gz.tbi, called/N_6490.contig-group-17.g.vcf.gz.tbi, called/N_690.contig-group-17.g.vcf.gz.tbi, called/N_1157.contig-group-17.g.vcf.gz, called/N_1157.contig-group-17.g.vcf.gz.tbi, called/T192.contig-group-17.g.vcf.gz.tbi, called/N_8171.contig-group-17.g.vcf.gz.tbi, called/N_1354.contig-group-17.g.vcf.gz, called/T192.contig-group-17.g.vcf.gz, called/N_4847.contig-group-17.g.vcf.gz.tbi, called/N_79.contig-group-17.g.vcf.gz, called/N_5129.contig-group-17.g.vcf.gz.tbi, called/T180.contig-group-17.g.vcf.gz, called/N_351.contig-group-17.g.vcf.gz, called/N_1927.contig-group-17.g.vcf.gz, called/N_1934_1_1_5973.contig-group-17.g.vcf.gz.tbi, called/N_1992_0123.contig-group-17.g.vcf.gz, called/T196.contig-group-17.g.vcf.gz, called/N_8565.contig-group-17.g.vcf.gz, called/N_2003_5409.contig-group-17.g.vcf.gz.tbi, called/N_351.contig-group-17.g.vcf.gz.tbi, called/N_689.contig-group-17.g.vcf.gz, called/N_5129.contig-group-17.g.vcf.gz, called/N_1354.contig-group-17.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-17.g.vcf.gz, called/N_1156.contig-group-17.g.vcf.gz, called/N_6928.contig-group-17.g.vcf.gz.tbi, called/T180.contig-group-17.g.vcf.gz.tbi, called/T187.contig-group-17.g.vcf.gz, called/N_8583.contig-group-17.g.vcf.gz.tbi, called/M5672.contig-group-17.g.vcf.gz.tbi, called/N_1386.contig-group-17.g.vcf.gz, called/T72.contig-group-17.g.vcf.gz.tbi, called/N_1386.contig-group-17.g.vcf.gz.tbi, called/N_1609.contig-group-17.g.vcf.gz.tbi, called/N_2003_5409.contig-group-17.g.vcf.gz, called/T79.contig-group-17.g.vcf.gz.tbi, called/N_4847.contig-group-17.g.vcf.gz, called/N_83.contig-group-17.g.vcf.gz.tbi, called/N_83.contig-group-17.g.vcf.gz, called/N_102.contig-group-17.g.vcf.gz, called/N_102.contig-group-17.g.vcf.gz.tbi, called/M5672.contig-group-17.g.vcf.gz, called/N_9449.contig-group-17.g.vcf.gz, called/T196.contig-group-17.g.vcf.gz.tbi, called/T187.contig-group-17.g.vcf.gz.tbi, called/N_9449.contig-group-17.g.vcf.gz.tbi, called/N_8565.contig-group-17.g.vcf.gz.tbi, called/N2005.contig-group-17.g.vcf.gz.tbi, called/N_6490.contig-group-17.g.vcf.gz, called/N_4843.contig-group-17.g.vcf.gz.tbi, called/T190.contig-group-17.g.vcf.gz.tbi, called/T79.contig-group-17.g.vcf.gz, called/N_1156.contig-group-17.g.vcf.gz.tbi, called/N_1927.contig-group-17.g.vcf.gz.tbi, called/N_4843.contig-group-17.g.vcf.gz, called/T1483.contig-group-17.g.vcf.gz.tbi, called/N_79.contig-group-17.g.vcf.gz.tbi, called/T1483.contig-group-17.g.vcf.gz, called/N_9104.contig-group-17.g.vcf.gz, called/N_1158.contig-group-17.g.vcf.gz, called/T185.contig-group-17.g.vcf.gz, called/T185.contig-group-17.g.vcf.gz.tbi, called/N_689.contig-group-17.g.vcf.gz.tbi, called/T72.contig-group-17.g.vcf.gz, called/N_690.contig-group-17.g.vcf.gz, called/N_6928.contig-group-17.g.vcf.gz, called/N_6489.contig-group-17.g.vcf.gz.tbi, called/N_8583.contig-group-17.g.vcf.gz, called/N_1609.contig-group-17.g.vcf.gz, called/N_9104.contig-group-17.g.vcf.gz.tbi, called/T190.contig-group-17.g.vcf.gz, called/N_8171.contig-group-17.g.vcf.gz, called/N_6489.contig-group-17.g.vcf.gz wildcards: contig=contig-group-17 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-10.g.vcf.gz, called/M1865_2.contig-group-10.g.vcf.gz, called/M5672.contig-group-10.g.vcf.gz, called/MTDC48361.contig-group-10.g.vcf.gz, called/N2005.contig-group-10.g.vcf.gz, called/N_102.contig-group-10.g.vcf.gz, called/N_1085.contig-group-10.g.vcf.gz, called/N_1156.contig-group-10.g.vcf.gz, called/N_1157.contig-group-10.g.vcf.gz, called/N_1158.contig-group-10.g.vcf.gz, called/N_1344.contig-group-10.g.vcf.gz, called/N_1347.contig-group-10.g.vcf.gz, called/N_1354.contig-group-10.g.vcf.gz, called/N_1355.contig-group-10.g.vcf.gz, called/N_1384.contig-group-10.g.vcf.gz, called/N_1386.contig-group-10.g.vcf.gz, called/N_1390.contig-group-10.g.vcf.gz, called/N_1409.contig-group-10.g.vcf.gz, called/N_1411.contig-group-10.g.vcf.gz, called/N_1413.contig-group-10.g.vcf.gz, called/N_1414.contig-group-10.g.vcf.gz, called/N_1609.contig-group-10.g.vcf.gz, called/N_1870.contig-group-10.g.vcf.gz, called/N_1901.contig-group-10.g.vcf.gz, called/N_1913.contig-group-10.g.vcf.gz, called/N_1927.contig-group-10.g.vcf.gz, called/N_192.contig-group-10.g.vcf.gz, called/N_1934_1_1_368.contig-group-10.g.vcf.gz, called/N_1934_1_1_5973.contig-group-10.g.vcf.gz, called/N_1951_13_1951.contig-group-10.g.vcf.gz, called/N_1992_0123.contig-group-10.g.vcf.gz, called/N_1998_0130.contig-group-10.g.vcf.gz, called/N_2001_0025.contig-group-10.g.vcf.gz, called/N_2001_0205.contig-group-10.g.vcf.gz, called/N_2002_0292.contig-group-10.g.vcf.gz, called/N_2003_5409.contig-group-10.g.vcf.gz, called/N_2004.contig-group-10.g.vcf.gz, called/N_2010_1759.contig-group-10.g.vcf.gz, called/N_21.contig-group-10.g.vcf.gz, called/N_351.contig-group-10.g.vcf.gz, called/N_355.contig-group-10.g.vcf.gz, called/N_401.contig-group-10.g.vcf.gz, called/N_403.contig-group-10.g.vcf.gz, called/N_4843.contig-group-10.g.vcf.gz, called/N_4844.contig-group-10.g.vcf.gz, called/N_4846.contig-group-10.g.vcf.gz, called/N_4847.contig-group-10.g.vcf.gz, called/N_5056.contig-group-10.g.vcf.gz, called/N_5057.contig-group-10.g.vcf.gz, called/N_5129.contig-group-10.g.vcf.gz, called/N_6489.contig-group-10.g.vcf.gz, called/N_6490.contig-group-10.g.vcf.gz, called/N_685.contig-group-10.g.vcf.gz, called/N_689.contig-group-10.g.vcf.gz, called/N_690.contig-group-10.g.vcf.gz, called/N_6926.contig-group-10.g.vcf.gz, called/N_6928.contig-group-10.g.vcf.gz, called/N_6932.contig-group-10.g.vcf.gz, called/N_6.contig-group-10.g.vcf.gz, called/N_7083.contig-group-10.g.vcf.gz, called/N_79.contig-group-10.g.vcf.gz, called/N_7.contig-group-10.g.vcf.gz, called/N_8105.contig-group-10.g.vcf.gz, called/N_8171.contig-group-10.g.vcf.gz, called/N_83.contig-group-10.g.vcf.gz, called/N_8564.contig-group-10.g.vcf.gz, called/N_8565.contig-group-10.g.vcf.gz, called/N_8583.contig-group-10.g.vcf.gz, called/N_8585.contig-group-10.g.vcf.gz, called/N_8586.contig-group-10.g.vcf.gz, called/N_9104.contig-group-10.g.vcf.gz, called/N_9449.contig-group-10.g.vcf.gz, called/N_94.contig-group-10.g.vcf.gz, called/T1481.contig-group-10.g.vcf.gz, called/T1483.contig-group-10.g.vcf.gz, called/T178.contig-group-10.g.vcf.gz, called/T179.contig-group-10.g.vcf.gz, called/T180.contig-group-10.g.vcf.gz, called/T181.contig-group-10.g.vcf.gz, called/T185.contig-group-10.g.vcf.gz, called/T186.contig-group-10.g.vcf.gz, called/T187.contig-group-10.g.vcf.gz, called/T188.contig-group-10.g.vcf.gz, called/T189.contig-group-10.g.vcf.gz, called/T190.contig-group-10.g.vcf.gz, called/T192.contig-group-10.g.vcf.gz, called/T193.contig-group-10.g.vcf.gz, called/T194.contig-group-10.g.vcf.gz, called/T196.contig-group-10.g.vcf.gz, called/T248.contig-group-10.g.vcf.gz, called/T37.contig-group-10.g.vcf.gz, called/T72.contig-group-10.g.vcf.gz, called/T79.contig-group-10.g.vcf.gz, called/M1864_2.contig-group-10.g.vcf.gz.tbi, called/M1865_2.contig-group-10.g.vcf.gz.tbi, called/M5672.contig-group-10.g.vcf.gz.tbi, called/MTDC48361.contig-group-10.g.vcf.gz.tbi, called/N2005.contig-group-10.g.vcf.gz.tbi, called/N_102.contig-group-10.g.vcf.gz.tbi, called/N_1085.contig-group-10.g.vcf.gz.tbi, called/N_1156.contig-group-10.g.vcf.gz.tbi, called/N_1157.contig-group-10.g.vcf.gz.tbi, called/N_1158.contig-group-10.g.vcf.gz.tbi, called/N_1344.contig-group-10.g.vcf.gz.tbi, called/N_1347.contig-group-10.g.vcf.gz.tbi, called/N_1354.contig-group-10.g.vcf.gz.tbi, called/N_1355.contig-group-10.g.vcf.gz.tbi, called/N_1384.contig-group-10.g.vcf.gz.tbi, called/N_1386.contig-group-10.g.vcf.gz.tbi, called/N_1390.contig-group-10.g.vcf.gz.tbi, called/N_1409.contig-group-10.g.vcf.gz.tbi, called/N_1411.contig-group-10.g.vcf.gz.tbi, called/N_1413.contig-group-10.g.vcf.gz.tbi, called/N_1414.contig-group-10.g.vcf.gz.tbi, called/N_1609.contig-group-10.g.vcf.gz.tbi, called/N_1870.contig-group-10.g.vcf.gz.tbi, called/N_1901.contig-group-10.g.vcf.gz.tbi, called/N_1913.contig-group-10.g.vcf.gz.tbi, called/N_1927.contig-group-10.g.vcf.gz.tbi, called/N_192.contig-group-10.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-10.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-10.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-10.g.vcf.gz.tbi, called/N_1992_0123.contig-group-10.g.vcf.gz.tbi, called/N_1998_0130.contig-group-10.g.vcf.gz.tbi, called/N_2001_0025.contig-group-10.g.vcf.gz.tbi, called/N_2001_0205.contig-group-10.g.vcf.gz.tbi, called/N_2002_0292.contig-group-10.g.vcf.gz.tbi, called/N_2003_5409.contig-group-10.g.vcf.gz.tbi, called/N_2004.contig-group-10.g.vcf.gz.tbi, called/N_2010_1759.contig-group-10.g.vcf.gz.tbi, called/N_21.contig-group-10.g.vcf.gz.tbi, called/N_351.contig-group-10.g.vcf.gz.tbi, called/N_355.contig-group-10.g.vcf.gz.tbi, called/N_401.contig-group-10.g.vcf.gz.tbi, called/N_403.contig-group-10.g.vcf.gz.tbi, called/N_4843.contig-group-10.g.vcf.gz.tbi, called/N_4844.contig-group-10.g.vcf.gz.tbi, called/N_4846.contig-group-10.g.vcf.gz.tbi, called/N_4847.contig-group-10.g.vcf.gz.tbi, called/N_5056.contig-group-10.g.vcf.gz.tbi, called/N_5057.contig-group-10.g.vcf.gz.tbi, called/N_5129.contig-group-10.g.vcf.gz.tbi, called/N_6489.contig-group-10.g.vcf.gz.tbi, called/N_6490.contig-group-10.g.vcf.gz.tbi, called/N_685.contig-group-10.g.vcf.gz.tbi, called/N_689.contig-group-10.g.vcf.gz.tbi, called/N_690.contig-group-10.g.vcf.gz.tbi, called/N_6926.contig-group-10.g.vcf.gz.tbi, called/N_6928.contig-group-10.g.vcf.gz.tbi, called/N_6932.contig-group-10.g.vcf.gz.tbi, called/N_6.contig-group-10.g.vcf.gz.tbi, called/N_7083.contig-group-10.g.vcf.gz.tbi, called/N_79.contig-group-10.g.vcf.gz.tbi, called/N_7.contig-group-10.g.vcf.gz.tbi, called/N_8105.contig-group-10.g.vcf.gz.tbi, called/N_8171.contig-group-10.g.vcf.gz.tbi, called/N_83.contig-group-10.g.vcf.gz.tbi, called/N_8564.contig-group-10.g.vcf.gz.tbi, called/N_8565.contig-group-10.g.vcf.gz.tbi, called/N_8583.contig-group-10.g.vcf.gz.tbi, called/N_8585.contig-group-10.g.vcf.gz.tbi, called/N_8586.contig-group-10.g.vcf.gz.tbi, called/N_9104.contig-group-10.g.vcf.gz.tbi, called/N_9449.contig-group-10.g.vcf.gz.tbi, called/N_94.contig-group-10.g.vcf.gz.tbi, called/T1481.contig-group-10.g.vcf.gz.tbi, called/T1483.contig-group-10.g.vcf.gz.tbi, called/T178.contig-group-10.g.vcf.gz.tbi, called/T179.contig-group-10.g.vcf.gz.tbi, called/T180.contig-group-10.g.vcf.gz.tbi, called/T181.contig-group-10.g.vcf.gz.tbi, called/T185.contig-group-10.g.vcf.gz.tbi, called/T186.contig-group-10.g.vcf.gz.tbi, called/T187.contig-group-10.g.vcf.gz.tbi, called/T188.contig-group-10.g.vcf.gz.tbi, called/T189.contig-group-10.g.vcf.gz.tbi, called/T190.contig-group-10.g.vcf.gz.tbi, called/T192.contig-group-10.g.vcf.gz.tbi, called/T193.contig-group-10.g.vcf.gz.tbi, called/T194.contig-group-10.g.vcf.gz.tbi, called/T196.contig-group-10.g.vcf.gz.tbi, called/T248.contig-group-10.g.vcf.gz.tbi, called/T37.contig-group-10.g.vcf.gz.tbi, called/T72.contig-group-10.g.vcf.gz.tbi, called/T79.contig-group-10.g.vcf.gz.tbi output: called/all.contig-group-10.g.vcf.gz, called/all.contig-group-10.g.done log: logs/gatk/combine-gvcfs/contig-group-10.log jobid: 2365 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-10.bench.log reason: Input files updated by another job: called/N_6489.contig-group-10.g.vcf.gz, called/M5672.contig-group-10.g.vcf.gz, called/N_1609.contig-group-10.g.vcf.gz.tbi, called/T187.contig-group-10.g.vcf.gz.tbi, called/N_1992_0123.contig-group-10.g.vcf.gz.tbi, called/N_1157.contig-group-10.g.vcf.gz.tbi, called/N_2003_5409.contig-group-10.g.vcf.gz.tbi, called/N_2003_5409.contig-group-10.g.vcf.gz, called/N_8583.contig-group-10.g.vcf.gz, called/N_690.contig-group-10.g.vcf.gz, called/N_1386.contig-group-10.g.vcf.gz, called/T1483.contig-group-10.g.vcf.gz.tbi, called/N_102.contig-group-10.g.vcf.gz.tbi, called/N_4847.contig-group-10.g.vcf.gz.tbi, called/N_79.contig-group-10.g.vcf.gz, called/N_351.contig-group-10.g.vcf.gz, called/N_1158.contig-group-10.g.vcf.gz, called/T190.contig-group-10.g.vcf.gz.tbi, called/T192.contig-group-10.g.vcf.gz, called/T79.contig-group-10.g.vcf.gz, called/T1483.contig-group-10.g.vcf.gz, called/M5672.contig-group-10.g.vcf.gz.tbi, called/N_1927.contig-group-10.g.vcf.gz, called/N_1157.contig-group-10.g.vcf.gz, called/N_102.contig-group-10.g.vcf.gz, called/N_4847.contig-group-10.g.vcf.gz, called/T190.contig-group-10.g.vcf.gz, called/N_9449.contig-group-10.g.vcf.gz, called/T196.contig-group-10.g.vcf.gz.tbi, called/N_1609.contig-group-10.g.vcf.gz, called/N2005.contig-group-10.g.vcf.gz, called/N2005.contig-group-10.g.vcf.gz.tbi, called/N_6928.contig-group-10.g.vcf.gz, called/N_9104.contig-group-10.g.vcf.gz, called/T79.contig-group-10.g.vcf.gz.tbi, called/N_9449.contig-group-10.g.vcf.gz.tbi, called/N_4843.contig-group-10.g.vcf.gz.tbi, called/T180.contig-group-10.g.vcf.gz, called/N_1386.contig-group-10.g.vcf.gz.tbi, called/T187.contig-group-10.g.vcf.gz, called/N_1870.contig-group-10.g.vcf.gz.tbi, called/N_8565.contig-group-10.g.vcf.gz.tbi, called/T196.contig-group-10.g.vcf.gz, called/T185.contig-group-10.g.vcf.gz.tbi, called/N_8171.contig-group-10.g.vcf.gz, called/N_1156.contig-group-10.g.vcf.gz.tbi, called/N_1158.contig-group-10.g.vcf.gz.tbi, called/N_5129.contig-group-10.g.vcf.gz, called/N_1870.contig-group-10.g.vcf.gz, called/N_8565.contig-group-10.g.vcf.gz, called/N_6490.contig-group-10.g.vcf.gz.tbi, called/N_9104.contig-group-10.g.vcf.gz.tbi, called/T72.contig-group-10.g.vcf.gz.tbi, called/N_79.contig-group-10.g.vcf.gz.tbi, called/N_1992_0123.contig-group-10.g.vcf.gz, called/T180.contig-group-10.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-10.g.vcf.gz.tbi, called/N_6490.contig-group-10.g.vcf.gz, called/N_4843.contig-group-10.g.vcf.gz, called/N_689.contig-group-10.g.vcf.gz, called/T72.contig-group-10.g.vcf.gz, called/N_1927.contig-group-10.g.vcf.gz.tbi, called/N_690.contig-group-10.g.vcf.gz.tbi, called/N_83.contig-group-10.g.vcf.gz, called/N_351.contig-group-10.g.vcf.gz.tbi, called/N_8583.contig-group-10.g.vcf.gz.tbi, called/N_6928.contig-group-10.g.vcf.gz.tbi, called/T185.contig-group-10.g.vcf.gz, called/N_1354.contig-group-10.g.vcf.gz.tbi, called/N_5129.contig-group-10.g.vcf.gz.tbi, called/N_8171.contig-group-10.g.vcf.gz.tbi, called/N_689.contig-group-10.g.vcf.gz.tbi, called/N_6489.contig-group-10.g.vcf.gz.tbi, called/N_1156.contig-group-10.g.vcf.gz, called/T192.contig-group-10.g.vcf.gz.tbi, called/N_1354.contig-group-10.g.vcf.gz, called/N_1934_1_1_5973.contig-group-10.g.vcf.gz, called/N_83.contig-group-10.g.vcf.gz.tbi wildcards: contig=contig-group-10 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-26.g.vcf.gz, called/M1865_2.contig-group-26.g.vcf.gz, called/M5672.contig-group-26.g.vcf.gz, called/MTDC48361.contig-group-26.g.vcf.gz, called/N2005.contig-group-26.g.vcf.gz, called/N_102.contig-group-26.g.vcf.gz, called/N_1085.contig-group-26.g.vcf.gz, called/N_1156.contig-group-26.g.vcf.gz, called/N_1157.contig-group-26.g.vcf.gz, called/N_1158.contig-group-26.g.vcf.gz, called/N_1344.contig-group-26.g.vcf.gz, called/N_1347.contig-group-26.g.vcf.gz, called/N_1354.contig-group-26.g.vcf.gz, called/N_1355.contig-group-26.g.vcf.gz, called/N_1384.contig-group-26.g.vcf.gz, called/N_1386.contig-group-26.g.vcf.gz, called/N_1390.contig-group-26.g.vcf.gz, called/N_1409.contig-group-26.g.vcf.gz, called/N_1411.contig-group-26.g.vcf.gz, called/N_1413.contig-group-26.g.vcf.gz, called/N_1414.contig-group-26.g.vcf.gz, called/N_1609.contig-group-26.g.vcf.gz, called/N_1870.contig-group-26.g.vcf.gz, called/N_1901.contig-group-26.g.vcf.gz, called/N_1913.contig-group-26.g.vcf.gz, called/N_1927.contig-group-26.g.vcf.gz, called/N_192.contig-group-26.g.vcf.gz, called/N_1934_1_1_368.contig-group-26.g.vcf.gz, called/N_1934_1_1_5973.contig-group-26.g.vcf.gz, called/N_1951_13_1951.contig-group-26.g.vcf.gz, called/N_1992_0123.contig-group-26.g.vcf.gz, called/N_1998_0130.contig-group-26.g.vcf.gz, called/N_2001_0025.contig-group-26.g.vcf.gz, called/N_2001_0205.contig-group-26.g.vcf.gz, called/N_2002_0292.contig-group-26.g.vcf.gz, called/N_2003_5409.contig-group-26.g.vcf.gz, called/N_2004.contig-group-26.g.vcf.gz, called/N_2010_1759.contig-group-26.g.vcf.gz, called/N_21.contig-group-26.g.vcf.gz, called/N_351.contig-group-26.g.vcf.gz, called/N_355.contig-group-26.g.vcf.gz, called/N_401.contig-group-26.g.vcf.gz, called/N_403.contig-group-26.g.vcf.gz, called/N_4843.contig-group-26.g.vcf.gz, called/N_4844.contig-group-26.g.vcf.gz, called/N_4846.contig-group-26.g.vcf.gz, called/N_4847.contig-group-26.g.vcf.gz, called/N_5056.contig-group-26.g.vcf.gz, called/N_5057.contig-group-26.g.vcf.gz, called/N_5129.contig-group-26.g.vcf.gz, called/N_6489.contig-group-26.g.vcf.gz, called/N_6490.contig-group-26.g.vcf.gz, called/N_685.contig-group-26.g.vcf.gz, called/N_689.contig-group-26.g.vcf.gz, called/N_690.contig-group-26.g.vcf.gz, called/N_6926.contig-group-26.g.vcf.gz, called/N_6928.contig-group-26.g.vcf.gz, called/N_6932.contig-group-26.g.vcf.gz, called/N_6.contig-group-26.g.vcf.gz, called/N_7083.contig-group-26.g.vcf.gz, called/N_79.contig-group-26.g.vcf.gz, called/N_7.contig-group-26.g.vcf.gz, called/N_8105.contig-group-26.g.vcf.gz, called/N_8171.contig-group-26.g.vcf.gz, called/N_83.contig-group-26.g.vcf.gz, called/N_8564.contig-group-26.g.vcf.gz, called/N_8565.contig-group-26.g.vcf.gz, called/N_8583.contig-group-26.g.vcf.gz, called/N_8585.contig-group-26.g.vcf.gz, called/N_8586.contig-group-26.g.vcf.gz, called/N_9104.contig-group-26.g.vcf.gz, called/N_9449.contig-group-26.g.vcf.gz, called/N_94.contig-group-26.g.vcf.gz, called/T1481.contig-group-26.g.vcf.gz, called/T1483.contig-group-26.g.vcf.gz, called/T178.contig-group-26.g.vcf.gz, called/T179.contig-group-26.g.vcf.gz, called/T180.contig-group-26.g.vcf.gz, called/T181.contig-group-26.g.vcf.gz, called/T185.contig-group-26.g.vcf.gz, called/T186.contig-group-26.g.vcf.gz, called/T187.contig-group-26.g.vcf.gz, called/T188.contig-group-26.g.vcf.gz, called/T189.contig-group-26.g.vcf.gz, called/T190.contig-group-26.g.vcf.gz, called/T192.contig-group-26.g.vcf.gz, called/T193.contig-group-26.g.vcf.gz, called/T194.contig-group-26.g.vcf.gz, called/T196.contig-group-26.g.vcf.gz, called/T248.contig-group-26.g.vcf.gz, called/T37.contig-group-26.g.vcf.gz, called/T72.contig-group-26.g.vcf.gz, called/T79.contig-group-26.g.vcf.gz, called/M1864_2.contig-group-26.g.vcf.gz.tbi, called/M1865_2.contig-group-26.g.vcf.gz.tbi, called/M5672.contig-group-26.g.vcf.gz.tbi, called/MTDC48361.contig-group-26.g.vcf.gz.tbi, called/N2005.contig-group-26.g.vcf.gz.tbi, called/N_102.contig-group-26.g.vcf.gz.tbi, called/N_1085.contig-group-26.g.vcf.gz.tbi, called/N_1156.contig-group-26.g.vcf.gz.tbi, called/N_1157.contig-group-26.g.vcf.gz.tbi, called/N_1158.contig-group-26.g.vcf.gz.tbi, called/N_1344.contig-group-26.g.vcf.gz.tbi, called/N_1347.contig-group-26.g.vcf.gz.tbi, called/N_1354.contig-group-26.g.vcf.gz.tbi, called/N_1355.contig-group-26.g.vcf.gz.tbi, called/N_1384.contig-group-26.g.vcf.gz.tbi, called/N_1386.contig-group-26.g.vcf.gz.tbi, called/N_1390.contig-group-26.g.vcf.gz.tbi, called/N_1409.contig-group-26.g.vcf.gz.tbi, called/N_1411.contig-group-26.g.vcf.gz.tbi, called/N_1413.contig-group-26.g.vcf.gz.tbi, called/N_1414.contig-group-26.g.vcf.gz.tbi, called/N_1609.contig-group-26.g.vcf.gz.tbi, called/N_1870.contig-group-26.g.vcf.gz.tbi, called/N_1901.contig-group-26.g.vcf.gz.tbi, called/N_1913.contig-group-26.g.vcf.gz.tbi, called/N_1927.contig-group-26.g.vcf.gz.tbi, called/N_192.contig-group-26.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-26.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-26.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-26.g.vcf.gz.tbi, called/N_1992_0123.contig-group-26.g.vcf.gz.tbi, called/N_1998_0130.contig-group-26.g.vcf.gz.tbi, called/N_2001_0025.contig-group-26.g.vcf.gz.tbi, called/N_2001_0205.contig-group-26.g.vcf.gz.tbi, called/N_2002_0292.contig-group-26.g.vcf.gz.tbi, called/N_2003_5409.contig-group-26.g.vcf.gz.tbi, called/N_2004.contig-group-26.g.vcf.gz.tbi, called/N_2010_1759.contig-group-26.g.vcf.gz.tbi, called/N_21.contig-group-26.g.vcf.gz.tbi, called/N_351.contig-group-26.g.vcf.gz.tbi, called/N_355.contig-group-26.g.vcf.gz.tbi, called/N_401.contig-group-26.g.vcf.gz.tbi, called/N_403.contig-group-26.g.vcf.gz.tbi, called/N_4843.contig-group-26.g.vcf.gz.tbi, called/N_4844.contig-group-26.g.vcf.gz.tbi, called/N_4846.contig-group-26.g.vcf.gz.tbi, called/N_4847.contig-group-26.g.vcf.gz.tbi, called/N_5056.contig-group-26.g.vcf.gz.tbi, called/N_5057.contig-group-26.g.vcf.gz.tbi, called/N_5129.contig-group-26.g.vcf.gz.tbi, called/N_6489.contig-group-26.g.vcf.gz.tbi, called/N_6490.contig-group-26.g.vcf.gz.tbi, called/N_685.contig-group-26.g.vcf.gz.tbi, called/N_689.contig-group-26.g.vcf.gz.tbi, called/N_690.contig-group-26.g.vcf.gz.tbi, called/N_6926.contig-group-26.g.vcf.gz.tbi, called/N_6928.contig-group-26.g.vcf.gz.tbi, called/N_6932.contig-group-26.g.vcf.gz.tbi, called/N_6.contig-group-26.g.vcf.gz.tbi, called/N_7083.contig-group-26.g.vcf.gz.tbi, called/N_79.contig-group-26.g.vcf.gz.tbi, called/N_7.contig-group-26.g.vcf.gz.tbi, called/N_8105.contig-group-26.g.vcf.gz.tbi, called/N_8171.contig-group-26.g.vcf.gz.tbi, called/N_83.contig-group-26.g.vcf.gz.tbi, called/N_8564.contig-group-26.g.vcf.gz.tbi, called/N_8565.contig-group-26.g.vcf.gz.tbi, called/N_8583.contig-group-26.g.vcf.gz.tbi, called/N_8585.contig-group-26.g.vcf.gz.tbi, called/N_8586.contig-group-26.g.vcf.gz.tbi, called/N_9104.contig-group-26.g.vcf.gz.tbi, called/N_9449.contig-group-26.g.vcf.gz.tbi, called/N_94.contig-group-26.g.vcf.gz.tbi, called/T1481.contig-group-26.g.vcf.gz.tbi, called/T1483.contig-group-26.g.vcf.gz.tbi, called/T178.contig-group-26.g.vcf.gz.tbi, called/T179.contig-group-26.g.vcf.gz.tbi, called/T180.contig-group-26.g.vcf.gz.tbi, called/T181.contig-group-26.g.vcf.gz.tbi, called/T185.contig-group-26.g.vcf.gz.tbi, called/T186.contig-group-26.g.vcf.gz.tbi, called/T187.contig-group-26.g.vcf.gz.tbi, called/T188.contig-group-26.g.vcf.gz.tbi, called/T189.contig-group-26.g.vcf.gz.tbi, called/T190.contig-group-26.g.vcf.gz.tbi, called/T192.contig-group-26.g.vcf.gz.tbi, called/T193.contig-group-26.g.vcf.gz.tbi, called/T194.contig-group-26.g.vcf.gz.tbi, called/T196.contig-group-26.g.vcf.gz.tbi, called/T248.contig-group-26.g.vcf.gz.tbi, called/T37.contig-group-26.g.vcf.gz.tbi, called/T72.contig-group-26.g.vcf.gz.tbi, called/T79.contig-group-26.g.vcf.gz.tbi output: called/all.contig-group-26.g.vcf.gz, called/all.contig-group-26.g.done log: logs/gatk/combine-gvcfs/contig-group-26.log jobid: 3901 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-26.bench.log reason: Input files updated by another job: called/T185.contig-group-26.g.vcf.gz.tbi, called/N_5129.contig-group-26.g.vcf.gz, called/N_8171.contig-group-26.g.vcf.gz, called/T196.contig-group-26.g.vcf.gz, called/N_4847.contig-group-26.g.vcf.gz.tbi, called/N_6490.contig-group-26.g.vcf.gz, called/N_9104.contig-group-26.g.vcf.gz.tbi, called/N_1609.contig-group-26.g.vcf.gz, called/N_9449.contig-group-26.g.vcf.gz.tbi, called/N_6490.contig-group-26.g.vcf.gz.tbi, called/N_79.contig-group-26.g.vcf.gz.tbi, called/N_689.contig-group-26.g.vcf.gz, called/N2005.contig-group-26.g.vcf.gz, called/N_1386.contig-group-26.g.vcf.gz.tbi, called/N_1992_0123.contig-group-26.g.vcf.gz.tbi, called/N_1870.contig-group-26.g.vcf.gz, called/N_8583.contig-group-26.g.vcf.gz.tbi, called/N_83.contig-group-26.g.vcf.gz.tbi, called/N_1386.contig-group-26.g.vcf.gz, called/N_4847.contig-group-26.g.vcf.gz, called/N_1354.contig-group-26.g.vcf.gz.tbi, called/T196.contig-group-26.g.vcf.gz.tbi, called/N_1609.contig-group-26.g.vcf.gz.tbi, called/N_6489.contig-group-26.g.vcf.gz, called/T190.contig-group-26.g.vcf.gz.tbi, called/N_8565.contig-group-26.g.vcf.gz, called/T192.contig-group-26.g.vcf.gz.tbi, called/N_8565.contig-group-26.g.vcf.gz.tbi, called/N_1992_0123.contig-group-26.g.vcf.gz, called/N_689.contig-group-26.g.vcf.gz.tbi, called/T1483.contig-group-26.g.vcf.gz, called/T180.contig-group-26.g.vcf.gz.tbi, called/N_690.contig-group-26.g.vcf.gz.tbi, called/T190.contig-group-26.g.vcf.gz, called/M5672.contig-group-26.g.vcf.gz.tbi, called/N_1927.contig-group-26.g.vcf.gz, called/T1483.contig-group-26.g.vcf.gz.tbi, called/N_4843.contig-group-26.g.vcf.gz.tbi, called/N_1156.contig-group-26.g.vcf.gz.tbi, called/N_6928.contig-group-26.g.vcf.gz.tbi, called/T192.contig-group-26.g.vcf.gz, called/N_1158.contig-group-26.g.vcf.gz, called/T72.contig-group-26.g.vcf.gz, called/N_1157.contig-group-26.g.vcf.gz.tbi, called/T187.contig-group-26.g.vcf.gz.tbi, called/N_1927.contig-group-26.g.vcf.gz.tbi, called/N_351.contig-group-26.g.vcf.gz, called/N_9449.contig-group-26.g.vcf.gz, called/N_690.contig-group-26.g.vcf.gz, called/N_1158.contig-group-26.g.vcf.gz.tbi, called/N_8583.contig-group-26.g.vcf.gz, called/N_83.contig-group-26.g.vcf.gz, called/N_1354.contig-group-26.g.vcf.gz, called/N_1156.contig-group-26.g.vcf.gz, called/N_1934_1_1_5973.contig-group-26.g.vcf.gz, called/N_102.contig-group-26.g.vcf.gz, called/T72.contig-group-26.g.vcf.gz.tbi, called/N_351.contig-group-26.g.vcf.gz.tbi, called/T79.contig-group-26.g.vcf.gz.tbi, called/N_2003_5409.contig-group-26.g.vcf.gz, called/N_1870.contig-group-26.g.vcf.gz.tbi, called/T180.contig-group-26.g.vcf.gz, called/N2005.contig-group-26.g.vcf.gz.tbi, called/N_2003_5409.contig-group-26.g.vcf.gz.tbi, called/M5672.contig-group-26.g.vcf.gz, called/N_8171.contig-group-26.g.vcf.gz.tbi, called/N_5129.contig-group-26.g.vcf.gz.tbi, called/N_6489.contig-group-26.g.vcf.gz.tbi, called/T79.contig-group-26.g.vcf.gz, called/T185.contig-group-26.g.vcf.gz, called/N_79.contig-group-26.g.vcf.gz, called/N_4843.contig-group-26.g.vcf.gz, called/N_102.contig-group-26.g.vcf.gz.tbi, called/N_1157.contig-group-26.g.vcf.gz, called/N_9104.contig-group-26.g.vcf.gz, called/T187.contig-group-26.g.vcf.gz, called/N_6928.contig-group-26.g.vcf.gz, called/N_1934_1_1_5973.contig-group-26.g.vcf.gz.tbi wildcards: contig=contig-group-26 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-15.g.vcf.gz, called/M1865_2.contig-group-15.g.vcf.gz, called/M5672.contig-group-15.g.vcf.gz, called/MTDC48361.contig-group-15.g.vcf.gz, called/N2005.contig-group-15.g.vcf.gz, called/N_102.contig-group-15.g.vcf.gz, called/N_1085.contig-group-15.g.vcf.gz, called/N_1156.contig-group-15.g.vcf.gz, called/N_1157.contig-group-15.g.vcf.gz, called/N_1158.contig-group-15.g.vcf.gz, called/N_1344.contig-group-15.g.vcf.gz, called/N_1347.contig-group-15.g.vcf.gz, called/N_1354.contig-group-15.g.vcf.gz, called/N_1355.contig-group-15.g.vcf.gz, called/N_1384.contig-group-15.g.vcf.gz, called/N_1386.contig-group-15.g.vcf.gz, called/N_1390.contig-group-15.g.vcf.gz, called/N_1409.contig-group-15.g.vcf.gz, called/N_1411.contig-group-15.g.vcf.gz, called/N_1413.contig-group-15.g.vcf.gz, called/N_1414.contig-group-15.g.vcf.gz, called/N_1609.contig-group-15.g.vcf.gz, called/N_1870.contig-group-15.g.vcf.gz, called/N_1901.contig-group-15.g.vcf.gz, called/N_1913.contig-group-15.g.vcf.gz, called/N_1927.contig-group-15.g.vcf.gz, called/N_192.contig-group-15.g.vcf.gz, called/N_1934_1_1_368.contig-group-15.g.vcf.gz, called/N_1934_1_1_5973.contig-group-15.g.vcf.gz, called/N_1951_13_1951.contig-group-15.g.vcf.gz, called/N_1992_0123.contig-group-15.g.vcf.gz, called/N_1998_0130.contig-group-15.g.vcf.gz, called/N_2001_0025.contig-group-15.g.vcf.gz, called/N_2001_0205.contig-group-15.g.vcf.gz, called/N_2002_0292.contig-group-15.g.vcf.gz, called/N_2003_5409.contig-group-15.g.vcf.gz, called/N_2004.contig-group-15.g.vcf.gz, called/N_2010_1759.contig-group-15.g.vcf.gz, called/N_21.contig-group-15.g.vcf.gz, called/N_351.contig-group-15.g.vcf.gz, called/N_355.contig-group-15.g.vcf.gz, called/N_401.contig-group-15.g.vcf.gz, called/N_403.contig-group-15.g.vcf.gz, called/N_4843.contig-group-15.g.vcf.gz, called/N_4844.contig-group-15.g.vcf.gz, called/N_4846.contig-group-15.g.vcf.gz, called/N_4847.contig-group-15.g.vcf.gz, called/N_5056.contig-group-15.g.vcf.gz, called/N_5057.contig-group-15.g.vcf.gz, called/N_5129.contig-group-15.g.vcf.gz, called/N_6489.contig-group-15.g.vcf.gz, called/N_6490.contig-group-15.g.vcf.gz, called/N_685.contig-group-15.g.vcf.gz, called/N_689.contig-group-15.g.vcf.gz, called/N_690.contig-group-15.g.vcf.gz, called/N_6926.contig-group-15.g.vcf.gz, called/N_6928.contig-group-15.g.vcf.gz, called/N_6932.contig-group-15.g.vcf.gz, called/N_6.contig-group-15.g.vcf.gz, called/N_7083.contig-group-15.g.vcf.gz, called/N_79.contig-group-15.g.vcf.gz, called/N_7.contig-group-15.g.vcf.gz, called/N_8105.contig-group-15.g.vcf.gz, called/N_8171.contig-group-15.g.vcf.gz, called/N_83.contig-group-15.g.vcf.gz, called/N_8564.contig-group-15.g.vcf.gz, called/N_8565.contig-group-15.g.vcf.gz, called/N_8583.contig-group-15.g.vcf.gz, called/N_8585.contig-group-15.g.vcf.gz, called/N_8586.contig-group-15.g.vcf.gz, called/N_9104.contig-group-15.g.vcf.gz, called/N_9449.contig-group-15.g.vcf.gz, called/N_94.contig-group-15.g.vcf.gz, called/T1481.contig-group-15.g.vcf.gz, called/T1483.contig-group-15.g.vcf.gz, called/T178.contig-group-15.g.vcf.gz, called/T179.contig-group-15.g.vcf.gz, called/T180.contig-group-15.g.vcf.gz, called/T181.contig-group-15.g.vcf.gz, called/T185.contig-group-15.g.vcf.gz, called/T186.contig-group-15.g.vcf.gz, called/T187.contig-group-15.g.vcf.gz, called/T188.contig-group-15.g.vcf.gz, called/T189.contig-group-15.g.vcf.gz, called/T190.contig-group-15.g.vcf.gz, called/T192.contig-group-15.g.vcf.gz, called/T193.contig-group-15.g.vcf.gz, called/T194.contig-group-15.g.vcf.gz, called/T196.contig-group-15.g.vcf.gz, called/T248.contig-group-15.g.vcf.gz, called/T37.contig-group-15.g.vcf.gz, called/T72.contig-group-15.g.vcf.gz, called/T79.contig-group-15.g.vcf.gz, called/M1864_2.contig-group-15.g.vcf.gz.tbi, called/M1865_2.contig-group-15.g.vcf.gz.tbi, called/M5672.contig-group-15.g.vcf.gz.tbi, called/MTDC48361.contig-group-15.g.vcf.gz.tbi, called/N2005.contig-group-15.g.vcf.gz.tbi, called/N_102.contig-group-15.g.vcf.gz.tbi, called/N_1085.contig-group-15.g.vcf.gz.tbi, called/N_1156.contig-group-15.g.vcf.gz.tbi, called/N_1157.contig-group-15.g.vcf.gz.tbi, called/N_1158.contig-group-15.g.vcf.gz.tbi, called/N_1344.contig-group-15.g.vcf.gz.tbi, called/N_1347.contig-group-15.g.vcf.gz.tbi, called/N_1354.contig-group-15.g.vcf.gz.tbi, called/N_1355.contig-group-15.g.vcf.gz.tbi, called/N_1384.contig-group-15.g.vcf.gz.tbi, called/N_1386.contig-group-15.g.vcf.gz.tbi, called/N_1390.contig-group-15.g.vcf.gz.tbi, called/N_1409.contig-group-15.g.vcf.gz.tbi, called/N_1411.contig-group-15.g.vcf.gz.tbi, called/N_1413.contig-group-15.g.vcf.gz.tbi, called/N_1414.contig-group-15.g.vcf.gz.tbi, called/N_1609.contig-group-15.g.vcf.gz.tbi, called/N_1870.contig-group-15.g.vcf.gz.tbi, called/N_1901.contig-group-15.g.vcf.gz.tbi, called/N_1913.contig-group-15.g.vcf.gz.tbi, called/N_1927.contig-group-15.g.vcf.gz.tbi, called/N_192.contig-group-15.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-15.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-15.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-15.g.vcf.gz.tbi, called/N_1992_0123.contig-group-15.g.vcf.gz.tbi, called/N_1998_0130.contig-group-15.g.vcf.gz.tbi, called/N_2001_0025.contig-group-15.g.vcf.gz.tbi, called/N_2001_0205.contig-group-15.g.vcf.gz.tbi, called/N_2002_0292.contig-group-15.g.vcf.gz.tbi, called/N_2003_5409.contig-group-15.g.vcf.gz.tbi, called/N_2004.contig-group-15.g.vcf.gz.tbi, called/N_2010_1759.contig-group-15.g.vcf.gz.tbi, called/N_21.contig-group-15.g.vcf.gz.tbi, called/N_351.contig-group-15.g.vcf.gz.tbi, called/N_355.contig-group-15.g.vcf.gz.tbi, called/N_401.contig-group-15.g.vcf.gz.tbi, called/N_403.contig-group-15.g.vcf.gz.tbi, called/N_4843.contig-group-15.g.vcf.gz.tbi, called/N_4844.contig-group-15.g.vcf.gz.tbi, called/N_4846.contig-group-15.g.vcf.gz.tbi, called/N_4847.contig-group-15.g.vcf.gz.tbi, called/N_5056.contig-group-15.g.vcf.gz.tbi, called/N_5057.contig-group-15.g.vcf.gz.tbi, called/N_5129.contig-group-15.g.vcf.gz.tbi, called/N_6489.contig-group-15.g.vcf.gz.tbi, called/N_6490.contig-group-15.g.vcf.gz.tbi, called/N_685.contig-group-15.g.vcf.gz.tbi, called/N_689.contig-group-15.g.vcf.gz.tbi, called/N_690.contig-group-15.g.vcf.gz.tbi, called/N_6926.contig-group-15.g.vcf.gz.tbi, called/N_6928.contig-group-15.g.vcf.gz.tbi, called/N_6932.contig-group-15.g.vcf.gz.tbi, called/N_6.contig-group-15.g.vcf.gz.tbi, called/N_7083.contig-group-15.g.vcf.gz.tbi, called/N_79.contig-group-15.g.vcf.gz.tbi, called/N_7.contig-group-15.g.vcf.gz.tbi, called/N_8105.contig-group-15.g.vcf.gz.tbi, called/N_8171.contig-group-15.g.vcf.gz.tbi, called/N_83.contig-group-15.g.vcf.gz.tbi, called/N_8564.contig-group-15.g.vcf.gz.tbi, called/N_8565.contig-group-15.g.vcf.gz.tbi, called/N_8583.contig-group-15.g.vcf.gz.tbi, called/N_8585.contig-group-15.g.vcf.gz.tbi, called/N_8586.contig-group-15.g.vcf.gz.tbi, called/N_9104.contig-group-15.g.vcf.gz.tbi, called/N_9449.contig-group-15.g.vcf.gz.tbi, called/N_94.contig-group-15.g.vcf.gz.tbi, called/T1481.contig-group-15.g.vcf.gz.tbi, called/T1483.contig-group-15.g.vcf.gz.tbi, called/T178.contig-group-15.g.vcf.gz.tbi, called/T179.contig-group-15.g.vcf.gz.tbi, called/T180.contig-group-15.g.vcf.gz.tbi, called/T181.contig-group-15.g.vcf.gz.tbi, called/T185.contig-group-15.g.vcf.gz.tbi, called/T186.contig-group-15.g.vcf.gz.tbi, called/T187.contig-group-15.g.vcf.gz.tbi, called/T188.contig-group-15.g.vcf.gz.tbi, called/T189.contig-group-15.g.vcf.gz.tbi, called/T190.contig-group-15.g.vcf.gz.tbi, called/T192.contig-group-15.g.vcf.gz.tbi, called/T193.contig-group-15.g.vcf.gz.tbi, called/T194.contig-group-15.g.vcf.gz.tbi, called/T196.contig-group-15.g.vcf.gz.tbi, called/T248.contig-group-15.g.vcf.gz.tbi, called/T37.contig-group-15.g.vcf.gz.tbi, called/T72.contig-group-15.g.vcf.gz.tbi, called/T79.contig-group-15.g.vcf.gz.tbi output: called/all.contig-group-15.g.vcf.gz, called/all.contig-group-15.g.done log: logs/gatk/combine-gvcfs/contig-group-15.log jobid: 2845 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-15.bench.log reason: Input files updated by another job: called/T1483.contig-group-15.g.vcf.gz.tbi, called/T180.contig-group-15.g.vcf.gz, called/N2005.contig-group-15.g.vcf.gz.tbi, called/N_2003_5409.contig-group-15.g.vcf.gz, called/T1483.contig-group-15.g.vcf.gz, called/N_102.contig-group-15.g.vcf.gz.tbi, called/N_1354.contig-group-15.g.vcf.gz, called/T192.contig-group-15.g.vcf.gz, called/T185.contig-group-15.g.vcf.gz, called/T185.contig-group-15.g.vcf.gz.tbi, called/T79.contig-group-15.g.vcf.gz, called/N_8565.contig-group-15.g.vcf.gz, called/N_8565.contig-group-15.g.vcf.gz.tbi, called/N_79.contig-group-15.g.vcf.gz.tbi, called/N_6928.contig-group-15.g.vcf.gz.tbi, called/N_1927.contig-group-15.g.vcf.gz.tbi, called/N_6490.contig-group-15.g.vcf.gz.tbi, called/N_8583.contig-group-15.g.vcf.gz.tbi, called/T79.contig-group-15.g.vcf.gz.tbi, called/N_351.contig-group-15.g.vcf.gz.tbi, called/N_8583.contig-group-15.g.vcf.gz, called/T72.contig-group-15.g.vcf.gz.tbi, called/N2005.contig-group-15.g.vcf.gz, called/N_1609.contig-group-15.g.vcf.gz, called/N_689.contig-group-15.g.vcf.gz.tbi, called/N_4847.contig-group-15.g.vcf.gz, called/N_83.contig-group-15.g.vcf.gz, called/T192.contig-group-15.g.vcf.gz.tbi, called/N_1992_0123.contig-group-15.g.vcf.gz, called/N_351.contig-group-15.g.vcf.gz, called/T196.contig-group-15.g.vcf.gz.tbi, called/N_102.contig-group-15.g.vcf.gz, called/M5672.contig-group-15.g.vcf.gz, called/T187.contig-group-15.g.vcf.gz, called/N_79.contig-group-15.g.vcf.gz, called/T190.contig-group-15.g.vcf.gz.tbi, called/N_1158.contig-group-15.g.vcf.gz.tbi, called/N_8171.contig-group-15.g.vcf.gz.tbi, called/N_6489.contig-group-15.g.vcf.gz.tbi, called/N_5129.contig-group-15.g.vcf.gz, called/T72.contig-group-15.g.vcf.gz, called/N_6489.contig-group-15.g.vcf.gz, called/N_690.contig-group-15.g.vcf.gz.tbi, called/N_4843.contig-group-15.g.vcf.gz, called/N_1927.contig-group-15.g.vcf.gz, called/N_6490.contig-group-15.g.vcf.gz, called/M5672.contig-group-15.g.vcf.gz.tbi, called/N_6928.contig-group-15.g.vcf.gz, called/N_9449.contig-group-15.g.vcf.gz, called/N_1870.contig-group-15.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-15.g.vcf.gz, called/N_1609.contig-group-15.g.vcf.gz.tbi, called/N_1157.contig-group-15.g.vcf.gz.tbi, called/N_4843.contig-group-15.g.vcf.gz.tbi, called/N_1386.contig-group-15.g.vcf.gz.tbi, called/N_1386.contig-group-15.g.vcf.gz, called/N_83.contig-group-15.g.vcf.gz.tbi, called/N_1156.contig-group-15.g.vcf.gz.tbi, called/N_689.contig-group-15.g.vcf.gz, called/N_4847.contig-group-15.g.vcf.gz.tbi, called/N_5129.contig-group-15.g.vcf.gz.tbi, called/T180.contig-group-15.g.vcf.gz.tbi, called/T187.contig-group-15.g.vcf.gz.tbi, called/T190.contig-group-15.g.vcf.gz, called/N_1992_0123.contig-group-15.g.vcf.gz.tbi, called/N_1870.contig-group-15.g.vcf.gz, called/T196.contig-group-15.g.vcf.gz, called/N_9104.contig-group-15.g.vcf.gz.tbi, called/N_1157.contig-group-15.g.vcf.gz, called/N_1156.contig-group-15.g.vcf.gz, called/N_9104.contig-group-15.g.vcf.gz, called/N_8171.contig-group-15.g.vcf.gz, called/N_1354.contig-group-15.g.vcf.gz.tbi, called/N_690.contig-group-15.g.vcf.gz, called/N_1934_1_1_5973.contig-group-15.g.vcf.gz.tbi, called/N_9449.contig-group-15.g.vcf.gz.tbi, called/N_2003_5409.contig-group-15.g.vcf.gz.tbi, called/N_1158.contig-group-15.g.vcf.gz wildcards: contig=contig-group-15 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-8.g.vcf.gz, called/M1865_2.contig-group-8.g.vcf.gz, called/M5672.contig-group-8.g.vcf.gz, called/MTDC48361.contig-group-8.g.vcf.gz, called/N2005.contig-group-8.g.vcf.gz, called/N_102.contig-group-8.g.vcf.gz, called/N_1085.contig-group-8.g.vcf.gz, called/N_1156.contig-group-8.g.vcf.gz, called/N_1157.contig-group-8.g.vcf.gz, called/N_1158.contig-group-8.g.vcf.gz, called/N_1344.contig-group-8.g.vcf.gz, called/N_1347.contig-group-8.g.vcf.gz, called/N_1354.contig-group-8.g.vcf.gz, called/N_1355.contig-group-8.g.vcf.gz, called/N_1384.contig-group-8.g.vcf.gz, called/N_1386.contig-group-8.g.vcf.gz, called/N_1390.contig-group-8.g.vcf.gz, called/N_1409.contig-group-8.g.vcf.gz, called/N_1411.contig-group-8.g.vcf.gz, called/N_1413.contig-group-8.g.vcf.gz, called/N_1414.contig-group-8.g.vcf.gz, called/N_1609.contig-group-8.g.vcf.gz, called/N_1870.contig-group-8.g.vcf.gz, called/N_1901.contig-group-8.g.vcf.gz, called/N_1913.contig-group-8.g.vcf.gz, called/N_1927.contig-group-8.g.vcf.gz, called/N_192.contig-group-8.g.vcf.gz, called/N_1934_1_1_368.contig-group-8.g.vcf.gz, called/N_1934_1_1_5973.contig-group-8.g.vcf.gz, called/N_1951_13_1951.contig-group-8.g.vcf.gz, called/N_1992_0123.contig-group-8.g.vcf.gz, called/N_1998_0130.contig-group-8.g.vcf.gz, called/N_2001_0025.contig-group-8.g.vcf.gz, called/N_2001_0205.contig-group-8.g.vcf.gz, called/N_2002_0292.contig-group-8.g.vcf.gz, called/N_2003_5409.contig-group-8.g.vcf.gz, called/N_2004.contig-group-8.g.vcf.gz, called/N_2010_1759.contig-group-8.g.vcf.gz, called/N_21.contig-group-8.g.vcf.gz, called/N_351.contig-group-8.g.vcf.gz, called/N_355.contig-group-8.g.vcf.gz, called/N_401.contig-group-8.g.vcf.gz, called/N_403.contig-group-8.g.vcf.gz, called/N_4843.contig-group-8.g.vcf.gz, called/N_4844.contig-group-8.g.vcf.gz, called/N_4846.contig-group-8.g.vcf.gz, called/N_4847.contig-group-8.g.vcf.gz, called/N_5056.contig-group-8.g.vcf.gz, called/N_5057.contig-group-8.g.vcf.gz, called/N_5129.contig-group-8.g.vcf.gz, called/N_6489.contig-group-8.g.vcf.gz, called/N_6490.contig-group-8.g.vcf.gz, called/N_685.contig-group-8.g.vcf.gz, called/N_689.contig-group-8.g.vcf.gz, called/N_690.contig-group-8.g.vcf.gz, called/N_6926.contig-group-8.g.vcf.gz, called/N_6928.contig-group-8.g.vcf.gz, called/N_6932.contig-group-8.g.vcf.gz, called/N_6.contig-group-8.g.vcf.gz, called/N_7083.contig-group-8.g.vcf.gz, called/N_79.contig-group-8.g.vcf.gz, called/N_7.contig-group-8.g.vcf.gz, called/N_8105.contig-group-8.g.vcf.gz, called/N_8171.contig-group-8.g.vcf.gz, called/N_83.contig-group-8.g.vcf.gz, called/N_8564.contig-group-8.g.vcf.gz, called/N_8565.contig-group-8.g.vcf.gz, called/N_8583.contig-group-8.g.vcf.gz, called/N_8585.contig-group-8.g.vcf.gz, called/N_8586.contig-group-8.g.vcf.gz, called/N_9104.contig-group-8.g.vcf.gz, called/N_9449.contig-group-8.g.vcf.gz, called/N_94.contig-group-8.g.vcf.gz, called/T1481.contig-group-8.g.vcf.gz, called/T1483.contig-group-8.g.vcf.gz, called/T178.contig-group-8.g.vcf.gz, called/T179.contig-group-8.g.vcf.gz, called/T180.contig-group-8.g.vcf.gz, called/T181.contig-group-8.g.vcf.gz, called/T185.contig-group-8.g.vcf.gz, called/T186.contig-group-8.g.vcf.gz, called/T187.contig-group-8.g.vcf.gz, called/T188.contig-group-8.g.vcf.gz, called/T189.contig-group-8.g.vcf.gz, called/T190.contig-group-8.g.vcf.gz, called/T192.contig-group-8.g.vcf.gz, called/T193.contig-group-8.g.vcf.gz, called/T194.contig-group-8.g.vcf.gz, called/T196.contig-group-8.g.vcf.gz, called/T248.contig-group-8.g.vcf.gz, called/T37.contig-group-8.g.vcf.gz, called/T72.contig-group-8.g.vcf.gz, called/T79.contig-group-8.g.vcf.gz, called/M1864_2.contig-group-8.g.vcf.gz.tbi, called/M1865_2.contig-group-8.g.vcf.gz.tbi, called/M5672.contig-group-8.g.vcf.gz.tbi, called/MTDC48361.contig-group-8.g.vcf.gz.tbi, called/N2005.contig-group-8.g.vcf.gz.tbi, called/N_102.contig-group-8.g.vcf.gz.tbi, called/N_1085.contig-group-8.g.vcf.gz.tbi, called/N_1156.contig-group-8.g.vcf.gz.tbi, called/N_1157.contig-group-8.g.vcf.gz.tbi, called/N_1158.contig-group-8.g.vcf.gz.tbi, called/N_1344.contig-group-8.g.vcf.gz.tbi, called/N_1347.contig-group-8.g.vcf.gz.tbi, called/N_1354.contig-group-8.g.vcf.gz.tbi, called/N_1355.contig-group-8.g.vcf.gz.tbi, called/N_1384.contig-group-8.g.vcf.gz.tbi, called/N_1386.contig-group-8.g.vcf.gz.tbi, called/N_1390.contig-group-8.g.vcf.gz.tbi, called/N_1409.contig-group-8.g.vcf.gz.tbi, called/N_1411.contig-group-8.g.vcf.gz.tbi, called/N_1413.contig-group-8.g.vcf.gz.tbi, called/N_1414.contig-group-8.g.vcf.gz.tbi, called/N_1609.contig-group-8.g.vcf.gz.tbi, called/N_1870.contig-group-8.g.vcf.gz.tbi, called/N_1901.contig-group-8.g.vcf.gz.tbi, called/N_1913.contig-group-8.g.vcf.gz.tbi, called/N_1927.contig-group-8.g.vcf.gz.tbi, called/N_192.contig-group-8.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-8.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-8.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-8.g.vcf.gz.tbi, called/N_1992_0123.contig-group-8.g.vcf.gz.tbi, called/N_1998_0130.contig-group-8.g.vcf.gz.tbi, called/N_2001_0025.contig-group-8.g.vcf.gz.tbi, called/N_2001_0205.contig-group-8.g.vcf.gz.tbi, called/N_2002_0292.contig-group-8.g.vcf.gz.tbi, called/N_2003_5409.contig-group-8.g.vcf.gz.tbi, called/N_2004.contig-group-8.g.vcf.gz.tbi, called/N_2010_1759.contig-group-8.g.vcf.gz.tbi, called/N_21.contig-group-8.g.vcf.gz.tbi, called/N_351.contig-group-8.g.vcf.gz.tbi, called/N_355.contig-group-8.g.vcf.gz.tbi, called/N_401.contig-group-8.g.vcf.gz.tbi, called/N_403.contig-group-8.g.vcf.gz.tbi, called/N_4843.contig-group-8.g.vcf.gz.tbi, called/N_4844.contig-group-8.g.vcf.gz.tbi, called/N_4846.contig-group-8.g.vcf.gz.tbi, called/N_4847.contig-group-8.g.vcf.gz.tbi, called/N_5056.contig-group-8.g.vcf.gz.tbi, called/N_5057.contig-group-8.g.vcf.gz.tbi, called/N_5129.contig-group-8.g.vcf.gz.tbi, called/N_6489.contig-group-8.g.vcf.gz.tbi, called/N_6490.contig-group-8.g.vcf.gz.tbi, called/N_685.contig-group-8.g.vcf.gz.tbi, called/N_689.contig-group-8.g.vcf.gz.tbi, called/N_690.contig-group-8.g.vcf.gz.tbi, called/N_6926.contig-group-8.g.vcf.gz.tbi, called/N_6928.contig-group-8.g.vcf.gz.tbi, called/N_6932.contig-group-8.g.vcf.gz.tbi, called/N_6.contig-group-8.g.vcf.gz.tbi, called/N_7083.contig-group-8.g.vcf.gz.tbi, called/N_79.contig-group-8.g.vcf.gz.tbi, called/N_7.contig-group-8.g.vcf.gz.tbi, called/N_8105.contig-group-8.g.vcf.gz.tbi, called/N_8171.contig-group-8.g.vcf.gz.tbi, called/N_83.contig-group-8.g.vcf.gz.tbi, called/N_8564.contig-group-8.g.vcf.gz.tbi, called/N_8565.contig-group-8.g.vcf.gz.tbi, called/N_8583.contig-group-8.g.vcf.gz.tbi, called/N_8585.contig-group-8.g.vcf.gz.tbi, called/N_8586.contig-group-8.g.vcf.gz.tbi, called/N_9104.contig-group-8.g.vcf.gz.tbi, called/N_9449.contig-group-8.g.vcf.gz.tbi, called/N_94.contig-group-8.g.vcf.gz.tbi, called/T1481.contig-group-8.g.vcf.gz.tbi, called/T1483.contig-group-8.g.vcf.gz.tbi, called/T178.contig-group-8.g.vcf.gz.tbi, called/T179.contig-group-8.g.vcf.gz.tbi, called/T180.contig-group-8.g.vcf.gz.tbi, called/T181.contig-group-8.g.vcf.gz.tbi, called/T185.contig-group-8.g.vcf.gz.tbi, called/T186.contig-group-8.g.vcf.gz.tbi, called/T187.contig-group-8.g.vcf.gz.tbi, called/T188.contig-group-8.g.vcf.gz.tbi, called/T189.contig-group-8.g.vcf.gz.tbi, called/T190.contig-group-8.g.vcf.gz.tbi, called/T192.contig-group-8.g.vcf.gz.tbi, called/T193.contig-group-8.g.vcf.gz.tbi, called/T194.contig-group-8.g.vcf.gz.tbi, called/T196.contig-group-8.g.vcf.gz.tbi, called/T248.contig-group-8.g.vcf.gz.tbi, called/T37.contig-group-8.g.vcf.gz.tbi, called/T72.contig-group-8.g.vcf.gz.tbi, called/T79.contig-group-8.g.vcf.gz.tbi output: called/all.contig-group-8.g.vcf.gz, called/all.contig-group-8.g.done log: logs/gatk/combine-gvcfs/contig-group-8.log jobid: 2173 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-8.bench.log reason: Input files updated by another job: called/N_6489.contig-group-8.g.vcf.gz.tbi, called/N_2003_5409.contig-group-8.g.vcf.gz.tbi, called/N_83.contig-group-8.g.vcf.gz.tbi, called/T79.contig-group-8.g.vcf.gz, called/T1483.contig-group-8.g.vcf.gz, called/N_1992_0123.contig-group-8.g.vcf.gz.tbi, called/M5672.contig-group-8.g.vcf.gz, called/M5672.contig-group-8.g.vcf.gz.tbi, called/N_8565.contig-group-8.g.vcf.gz, called/N_690.contig-group-8.g.vcf.gz, called/N_9104.contig-group-8.g.vcf.gz.tbi, called/N_9449.contig-group-8.g.vcf.gz, called/N_6928.contig-group-8.g.vcf.gz.tbi, called/N_83.contig-group-8.g.vcf.gz, called/N_4843.contig-group-8.g.vcf.gz, called/N_1157.contig-group-8.g.vcf.gz, called/N_8583.contig-group-8.g.vcf.gz.tbi, called/N_1354.contig-group-8.g.vcf.gz.tbi, called/T1483.contig-group-8.g.vcf.gz.tbi, called/N_6490.contig-group-8.g.vcf.gz.tbi, called/N_5129.contig-group-8.g.vcf.gz, called/N_1927.contig-group-8.g.vcf.gz, called/N_690.contig-group-8.g.vcf.gz.tbi, called/N2005.contig-group-8.g.vcf.gz, called/N_1158.contig-group-8.g.vcf.gz.tbi, called/N_1156.contig-group-8.g.vcf.gz, called/N_1934_1_1_5973.contig-group-8.g.vcf.gz.tbi, called/T192.contig-group-8.g.vcf.gz, called/T196.contig-group-8.g.vcf.gz.tbi, called/N_79.contig-group-8.g.vcf.gz, called/N_8171.contig-group-8.g.vcf.gz, called/N_1386.contig-group-8.g.vcf.gz.tbi, called/N_1156.contig-group-8.g.vcf.gz.tbi, called/N_6490.contig-group-8.g.vcf.gz, called/T79.contig-group-8.g.vcf.gz.tbi, called/T72.contig-group-8.g.vcf.gz, called/N_4847.contig-group-8.g.vcf.gz.tbi, called/N_102.contig-group-8.g.vcf.gz.tbi, called/N_351.contig-group-8.g.vcf.gz, called/N2005.contig-group-8.g.vcf.gz.tbi, called/N_1927.contig-group-8.g.vcf.gz.tbi, called/N_1870.contig-group-8.g.vcf.gz, called/N_79.contig-group-8.g.vcf.gz.tbi, called/T187.contig-group-8.g.vcf.gz.tbi, called/T192.contig-group-8.g.vcf.gz.tbi, called/T196.contig-group-8.g.vcf.gz, called/N_689.contig-group-8.g.vcf.gz.tbi, called/N_9449.contig-group-8.g.vcf.gz.tbi, called/T185.contig-group-8.g.vcf.gz.tbi, called/T180.contig-group-8.g.vcf.gz, called/N_1354.contig-group-8.g.vcf.gz, called/N_1609.contig-group-8.g.vcf.gz, called/N_5129.contig-group-8.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-8.g.vcf.gz, called/N_1992_0123.contig-group-8.g.vcf.gz, called/N_1386.contig-group-8.g.vcf.gz, called/N_1609.contig-group-8.g.vcf.gz.tbi, called/T180.contig-group-8.g.vcf.gz.tbi, called/N_2003_5409.contig-group-8.g.vcf.gz, called/N_6489.contig-group-8.g.vcf.gz, called/T72.contig-group-8.g.vcf.gz.tbi, called/N_9104.contig-group-8.g.vcf.gz, called/N_8583.contig-group-8.g.vcf.gz, called/N_6928.contig-group-8.g.vcf.gz, called/N_351.contig-group-8.g.vcf.gz.tbi, called/N_102.contig-group-8.g.vcf.gz, called/N_1157.contig-group-8.g.vcf.gz.tbi, called/N_1870.contig-group-8.g.vcf.gz.tbi, called/N_4847.contig-group-8.g.vcf.gz, called/N_8565.contig-group-8.g.vcf.gz.tbi, called/T187.contig-group-8.g.vcf.gz, called/T185.contig-group-8.g.vcf.gz, called/T190.contig-group-8.g.vcf.gz.tbi, called/N_8171.contig-group-8.g.vcf.gz.tbi, called/N_1158.contig-group-8.g.vcf.gz, called/N_689.contig-group-8.g.vcf.gz, called/N_4843.contig-group-8.g.vcf.gz.tbi, called/T190.contig-group-8.g.vcf.gz wildcards: contig=contig-group-8 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-22.g.vcf.gz, called/M1865_2.contig-group-22.g.vcf.gz, called/M5672.contig-group-22.g.vcf.gz, called/MTDC48361.contig-group-22.g.vcf.gz, called/N2005.contig-group-22.g.vcf.gz, called/N_102.contig-group-22.g.vcf.gz, called/N_1085.contig-group-22.g.vcf.gz, called/N_1156.contig-group-22.g.vcf.gz, called/N_1157.contig-group-22.g.vcf.gz, called/N_1158.contig-group-22.g.vcf.gz, called/N_1344.contig-group-22.g.vcf.gz, called/N_1347.contig-group-22.g.vcf.gz, called/N_1354.contig-group-22.g.vcf.gz, called/N_1355.contig-group-22.g.vcf.gz, called/N_1384.contig-group-22.g.vcf.gz, called/N_1386.contig-group-22.g.vcf.gz, called/N_1390.contig-group-22.g.vcf.gz, called/N_1409.contig-group-22.g.vcf.gz, called/N_1411.contig-group-22.g.vcf.gz, called/N_1413.contig-group-22.g.vcf.gz, called/N_1414.contig-group-22.g.vcf.gz, called/N_1609.contig-group-22.g.vcf.gz, called/N_1870.contig-group-22.g.vcf.gz, called/N_1901.contig-group-22.g.vcf.gz, called/N_1913.contig-group-22.g.vcf.gz, called/N_1927.contig-group-22.g.vcf.gz, called/N_192.contig-group-22.g.vcf.gz, called/N_1934_1_1_368.contig-group-22.g.vcf.gz, called/N_1934_1_1_5973.contig-group-22.g.vcf.gz, called/N_1951_13_1951.contig-group-22.g.vcf.gz, called/N_1992_0123.contig-group-22.g.vcf.gz, called/N_1998_0130.contig-group-22.g.vcf.gz, called/N_2001_0025.contig-group-22.g.vcf.gz, called/N_2001_0205.contig-group-22.g.vcf.gz, called/N_2002_0292.contig-group-22.g.vcf.gz, called/N_2003_5409.contig-group-22.g.vcf.gz, called/N_2004.contig-group-22.g.vcf.gz, called/N_2010_1759.contig-group-22.g.vcf.gz, called/N_21.contig-group-22.g.vcf.gz, called/N_351.contig-group-22.g.vcf.gz, called/N_355.contig-group-22.g.vcf.gz, called/N_401.contig-group-22.g.vcf.gz, called/N_403.contig-group-22.g.vcf.gz, called/N_4843.contig-group-22.g.vcf.gz, called/N_4844.contig-group-22.g.vcf.gz, called/N_4846.contig-group-22.g.vcf.gz, called/N_4847.contig-group-22.g.vcf.gz, called/N_5056.contig-group-22.g.vcf.gz, called/N_5057.contig-group-22.g.vcf.gz, called/N_5129.contig-group-22.g.vcf.gz, called/N_6489.contig-group-22.g.vcf.gz, called/N_6490.contig-group-22.g.vcf.gz, called/N_685.contig-group-22.g.vcf.gz, called/N_689.contig-group-22.g.vcf.gz, called/N_690.contig-group-22.g.vcf.gz, called/N_6926.contig-group-22.g.vcf.gz, called/N_6928.contig-group-22.g.vcf.gz, called/N_6932.contig-group-22.g.vcf.gz, called/N_6.contig-group-22.g.vcf.gz, called/N_7083.contig-group-22.g.vcf.gz, called/N_79.contig-group-22.g.vcf.gz, called/N_7.contig-group-22.g.vcf.gz, called/N_8105.contig-group-22.g.vcf.gz, called/N_8171.contig-group-22.g.vcf.gz, called/N_83.contig-group-22.g.vcf.gz, called/N_8564.contig-group-22.g.vcf.gz, called/N_8565.contig-group-22.g.vcf.gz, called/N_8583.contig-group-22.g.vcf.gz, called/N_8585.contig-group-22.g.vcf.gz, called/N_8586.contig-group-22.g.vcf.gz, called/N_9104.contig-group-22.g.vcf.gz, called/N_9449.contig-group-22.g.vcf.gz, called/N_94.contig-group-22.g.vcf.gz, called/T1481.contig-group-22.g.vcf.gz, called/T1483.contig-group-22.g.vcf.gz, called/T178.contig-group-22.g.vcf.gz, called/T179.contig-group-22.g.vcf.gz, called/T180.contig-group-22.g.vcf.gz, called/T181.contig-group-22.g.vcf.gz, called/T185.contig-group-22.g.vcf.gz, called/T186.contig-group-22.g.vcf.gz, called/T187.contig-group-22.g.vcf.gz, called/T188.contig-group-22.g.vcf.gz, called/T189.contig-group-22.g.vcf.gz, called/T190.contig-group-22.g.vcf.gz, called/T192.contig-group-22.g.vcf.gz, called/T193.contig-group-22.g.vcf.gz, called/T194.contig-group-22.g.vcf.gz, called/T196.contig-group-22.g.vcf.gz, called/T248.contig-group-22.g.vcf.gz, called/T37.contig-group-22.g.vcf.gz, called/T72.contig-group-22.g.vcf.gz, called/T79.contig-group-22.g.vcf.gz, called/M1864_2.contig-group-22.g.vcf.gz.tbi, called/M1865_2.contig-group-22.g.vcf.gz.tbi, called/M5672.contig-group-22.g.vcf.gz.tbi, called/MTDC48361.contig-group-22.g.vcf.gz.tbi, called/N2005.contig-group-22.g.vcf.gz.tbi, called/N_102.contig-group-22.g.vcf.gz.tbi, called/N_1085.contig-group-22.g.vcf.gz.tbi, called/N_1156.contig-group-22.g.vcf.gz.tbi, called/N_1157.contig-group-22.g.vcf.gz.tbi, called/N_1158.contig-group-22.g.vcf.gz.tbi, called/N_1344.contig-group-22.g.vcf.gz.tbi, called/N_1347.contig-group-22.g.vcf.gz.tbi, called/N_1354.contig-group-22.g.vcf.gz.tbi, called/N_1355.contig-group-22.g.vcf.gz.tbi, called/N_1384.contig-group-22.g.vcf.gz.tbi, called/N_1386.contig-group-22.g.vcf.gz.tbi, called/N_1390.contig-group-22.g.vcf.gz.tbi, called/N_1409.contig-group-22.g.vcf.gz.tbi, called/N_1411.contig-group-22.g.vcf.gz.tbi, called/N_1413.contig-group-22.g.vcf.gz.tbi, called/N_1414.contig-group-22.g.vcf.gz.tbi, called/N_1609.contig-group-22.g.vcf.gz.tbi, called/N_1870.contig-group-22.g.vcf.gz.tbi, called/N_1901.contig-group-22.g.vcf.gz.tbi, called/N_1913.contig-group-22.g.vcf.gz.tbi, called/N_1927.contig-group-22.g.vcf.gz.tbi, called/N_192.contig-group-22.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-22.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-22.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-22.g.vcf.gz.tbi, called/N_1992_0123.contig-group-22.g.vcf.gz.tbi, called/N_1998_0130.contig-group-22.g.vcf.gz.tbi, called/N_2001_0025.contig-group-22.g.vcf.gz.tbi, called/N_2001_0205.contig-group-22.g.vcf.gz.tbi, called/N_2002_0292.contig-group-22.g.vcf.gz.tbi, called/N_2003_5409.contig-group-22.g.vcf.gz.tbi, called/N_2004.contig-group-22.g.vcf.gz.tbi, called/N_2010_1759.contig-group-22.g.vcf.gz.tbi, called/N_21.contig-group-22.g.vcf.gz.tbi, called/N_351.contig-group-22.g.vcf.gz.tbi, called/N_355.contig-group-22.g.vcf.gz.tbi, called/N_401.contig-group-22.g.vcf.gz.tbi, called/N_403.contig-group-22.g.vcf.gz.tbi, called/N_4843.contig-group-22.g.vcf.gz.tbi, called/N_4844.contig-group-22.g.vcf.gz.tbi, called/N_4846.contig-group-22.g.vcf.gz.tbi, called/N_4847.contig-group-22.g.vcf.gz.tbi, called/N_5056.contig-group-22.g.vcf.gz.tbi, called/N_5057.contig-group-22.g.vcf.gz.tbi, called/N_5129.contig-group-22.g.vcf.gz.tbi, called/N_6489.contig-group-22.g.vcf.gz.tbi, called/N_6490.contig-group-22.g.vcf.gz.tbi, called/N_685.contig-group-22.g.vcf.gz.tbi, called/N_689.contig-group-22.g.vcf.gz.tbi, called/N_690.contig-group-22.g.vcf.gz.tbi, called/N_6926.contig-group-22.g.vcf.gz.tbi, called/N_6928.contig-group-22.g.vcf.gz.tbi, called/N_6932.contig-group-22.g.vcf.gz.tbi, called/N_6.contig-group-22.g.vcf.gz.tbi, called/N_7083.contig-group-22.g.vcf.gz.tbi, called/N_79.contig-group-22.g.vcf.gz.tbi, called/N_7.contig-group-22.g.vcf.gz.tbi, called/N_8105.contig-group-22.g.vcf.gz.tbi, called/N_8171.contig-group-22.g.vcf.gz.tbi, called/N_83.contig-group-22.g.vcf.gz.tbi, called/N_8564.contig-group-22.g.vcf.gz.tbi, called/N_8565.contig-group-22.g.vcf.gz.tbi, called/N_8583.contig-group-22.g.vcf.gz.tbi, called/N_8585.contig-group-22.g.vcf.gz.tbi, called/N_8586.contig-group-22.g.vcf.gz.tbi, called/N_9104.contig-group-22.g.vcf.gz.tbi, called/N_9449.contig-group-22.g.vcf.gz.tbi, called/N_94.contig-group-22.g.vcf.gz.tbi, called/T1481.contig-group-22.g.vcf.gz.tbi, called/T1483.contig-group-22.g.vcf.gz.tbi, called/T178.contig-group-22.g.vcf.gz.tbi, called/T179.contig-group-22.g.vcf.gz.tbi, called/T180.contig-group-22.g.vcf.gz.tbi, called/T181.contig-group-22.g.vcf.gz.tbi, called/T185.contig-group-22.g.vcf.gz.tbi, called/T186.contig-group-22.g.vcf.gz.tbi, called/T187.contig-group-22.g.vcf.gz.tbi, called/T188.contig-group-22.g.vcf.gz.tbi, called/T189.contig-group-22.g.vcf.gz.tbi, called/T190.contig-group-22.g.vcf.gz.tbi, called/T192.contig-group-22.g.vcf.gz.tbi, called/T193.contig-group-22.g.vcf.gz.tbi, called/T194.contig-group-22.g.vcf.gz.tbi, called/T196.contig-group-22.g.vcf.gz.tbi, called/T248.contig-group-22.g.vcf.gz.tbi, called/T37.contig-group-22.g.vcf.gz.tbi, called/T72.contig-group-22.g.vcf.gz.tbi, called/T79.contig-group-22.g.vcf.gz.tbi output: called/all.contig-group-22.g.vcf.gz, called/all.contig-group-22.g.done log: logs/gatk/combine-gvcfs/contig-group-22.log jobid: 3517 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-22.bench.log reason: Input files updated by another job: called/T79.contig-group-22.g.vcf.gz.tbi, called/N_1927.contig-group-22.g.vcf.gz.tbi, called/T192.contig-group-22.g.vcf.gz, called/N_689.contig-group-22.g.vcf.gz.tbi, called/N_1158.contig-group-22.g.vcf.gz, called/N_1934_1_1_5973.contig-group-22.g.vcf.gz.tbi, called/T190.contig-group-22.g.vcf.gz, called/M5672.contig-group-22.g.vcf.gz.tbi, called/N_6928.contig-group-22.g.vcf.gz.tbi, called/N_8583.contig-group-22.g.vcf.gz, called/T196.contig-group-22.g.vcf.gz.tbi, called/N_6489.contig-group-22.g.vcf.gz, called/N_9449.contig-group-22.g.vcf.gz.tbi, called/N_1157.contig-group-22.g.vcf.gz, called/N_1609.contig-group-22.g.vcf.gz, called/T187.contig-group-22.g.vcf.gz.tbi, called/N_83.contig-group-22.g.vcf.gz.tbi, called/N_79.contig-group-22.g.vcf.gz.tbi, called/T1483.contig-group-22.g.vcf.gz, called/N_1156.contig-group-22.g.vcf.gz.tbi, called/T72.contig-group-22.g.vcf.gz, called/N_5129.contig-group-22.g.vcf.gz, called/N_2003_5409.contig-group-22.g.vcf.gz.tbi, called/N_1992_0123.contig-group-22.g.vcf.gz, called/N_1157.contig-group-22.g.vcf.gz.tbi, called/N_690.contig-group-22.g.vcf.gz, called/N_1992_0123.contig-group-22.g.vcf.gz.tbi, called/N_6490.contig-group-22.g.vcf.gz, called/N_1386.contig-group-22.g.vcf.gz, called/N_1870.contig-group-22.g.vcf.gz.tbi, called/N_6490.contig-group-22.g.vcf.gz.tbi, called/N_1354.contig-group-22.g.vcf.gz, called/N_4843.contig-group-22.g.vcf.gz.tbi, called/T1483.contig-group-22.g.vcf.gz.tbi, called/T190.contig-group-22.g.vcf.gz.tbi, called/N2005.contig-group-22.g.vcf.gz, called/N_5129.contig-group-22.g.vcf.gz.tbi, called/N_83.contig-group-22.g.vcf.gz, called/N_689.contig-group-22.g.vcf.gz, called/N_9449.contig-group-22.g.vcf.gz, called/T180.contig-group-22.g.vcf.gz, called/N_1934_1_1_5973.contig-group-22.g.vcf.gz, called/N_1158.contig-group-22.g.vcf.gz.tbi, called/N_8565.contig-group-22.g.vcf.gz, called/N_102.contig-group-22.g.vcf.gz.tbi, called/N_1386.contig-group-22.g.vcf.gz.tbi, called/N_6489.contig-group-22.g.vcf.gz.tbi, called/N_1354.contig-group-22.g.vcf.gz.tbi, called/N_1870.contig-group-22.g.vcf.gz, called/N_1927.contig-group-22.g.vcf.gz, called/N_9104.contig-group-22.g.vcf.gz.tbi, called/T180.contig-group-22.g.vcf.gz.tbi, called/N_351.contig-group-22.g.vcf.gz.tbi, called/N_8171.contig-group-22.g.vcf.gz, called/N_8583.contig-group-22.g.vcf.gz.tbi, called/N_2003_5409.contig-group-22.g.vcf.gz, called/T72.contig-group-22.g.vcf.gz.tbi, called/N_8171.contig-group-22.g.vcf.gz.tbi, called/N_1156.contig-group-22.g.vcf.gz, called/N_351.contig-group-22.g.vcf.gz, called/N_6928.contig-group-22.g.vcf.gz, called/T187.contig-group-22.g.vcf.gz, called/T192.contig-group-22.g.vcf.gz.tbi, called/N2005.contig-group-22.g.vcf.gz.tbi, called/T79.contig-group-22.g.vcf.gz, called/N_4847.contig-group-22.g.vcf.gz.tbi, called/T185.contig-group-22.g.vcf.gz, called/N_102.contig-group-22.g.vcf.gz, called/T185.contig-group-22.g.vcf.gz.tbi, called/N_690.contig-group-22.g.vcf.gz.tbi, called/N_4847.contig-group-22.g.vcf.gz, called/N_79.contig-group-22.g.vcf.gz, called/M5672.contig-group-22.g.vcf.gz, called/N_8565.contig-group-22.g.vcf.gz.tbi, called/T196.contig-group-22.g.vcf.gz, called/N_4843.contig-group-22.g.vcf.gz, called/N_1609.contig-group-22.g.vcf.gz.tbi, called/N_9104.contig-group-22.g.vcf.gz wildcards: contig=contig-group-22 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-19.g.vcf.gz, called/M1865_2.contig-group-19.g.vcf.gz, called/M5672.contig-group-19.g.vcf.gz, called/MTDC48361.contig-group-19.g.vcf.gz, called/N2005.contig-group-19.g.vcf.gz, called/N_102.contig-group-19.g.vcf.gz, called/N_1085.contig-group-19.g.vcf.gz, called/N_1156.contig-group-19.g.vcf.gz, called/N_1157.contig-group-19.g.vcf.gz, called/N_1158.contig-group-19.g.vcf.gz, called/N_1344.contig-group-19.g.vcf.gz, called/N_1347.contig-group-19.g.vcf.gz, called/N_1354.contig-group-19.g.vcf.gz, called/N_1355.contig-group-19.g.vcf.gz, called/N_1384.contig-group-19.g.vcf.gz, called/N_1386.contig-group-19.g.vcf.gz, called/N_1390.contig-group-19.g.vcf.gz, called/N_1409.contig-group-19.g.vcf.gz, called/N_1411.contig-group-19.g.vcf.gz, called/N_1413.contig-group-19.g.vcf.gz, called/N_1414.contig-group-19.g.vcf.gz, called/N_1609.contig-group-19.g.vcf.gz, called/N_1870.contig-group-19.g.vcf.gz, called/N_1901.contig-group-19.g.vcf.gz, called/N_1913.contig-group-19.g.vcf.gz, called/N_1927.contig-group-19.g.vcf.gz, called/N_192.contig-group-19.g.vcf.gz, called/N_1934_1_1_368.contig-group-19.g.vcf.gz, called/N_1934_1_1_5973.contig-group-19.g.vcf.gz, called/N_1951_13_1951.contig-group-19.g.vcf.gz, called/N_1992_0123.contig-group-19.g.vcf.gz, called/N_1998_0130.contig-group-19.g.vcf.gz, called/N_2001_0025.contig-group-19.g.vcf.gz, called/N_2001_0205.contig-group-19.g.vcf.gz, called/N_2002_0292.contig-group-19.g.vcf.gz, called/N_2003_5409.contig-group-19.g.vcf.gz, called/N_2004.contig-group-19.g.vcf.gz, called/N_2010_1759.contig-group-19.g.vcf.gz, called/N_21.contig-group-19.g.vcf.gz, called/N_351.contig-group-19.g.vcf.gz, called/N_355.contig-group-19.g.vcf.gz, called/N_401.contig-group-19.g.vcf.gz, called/N_403.contig-group-19.g.vcf.gz, called/N_4843.contig-group-19.g.vcf.gz, called/N_4844.contig-group-19.g.vcf.gz, called/N_4846.contig-group-19.g.vcf.gz, called/N_4847.contig-group-19.g.vcf.gz, called/N_5056.contig-group-19.g.vcf.gz, called/N_5057.contig-group-19.g.vcf.gz, called/N_5129.contig-group-19.g.vcf.gz, called/N_6489.contig-group-19.g.vcf.gz, called/N_6490.contig-group-19.g.vcf.gz, called/N_685.contig-group-19.g.vcf.gz, called/N_689.contig-group-19.g.vcf.gz, called/N_690.contig-group-19.g.vcf.gz, called/N_6926.contig-group-19.g.vcf.gz, called/N_6928.contig-group-19.g.vcf.gz, called/N_6932.contig-group-19.g.vcf.gz, called/N_6.contig-group-19.g.vcf.gz, called/N_7083.contig-group-19.g.vcf.gz, called/N_79.contig-group-19.g.vcf.gz, called/N_7.contig-group-19.g.vcf.gz, called/N_8105.contig-group-19.g.vcf.gz, called/N_8171.contig-group-19.g.vcf.gz, called/N_83.contig-group-19.g.vcf.gz, called/N_8564.contig-group-19.g.vcf.gz, called/N_8565.contig-group-19.g.vcf.gz, called/N_8583.contig-group-19.g.vcf.gz, called/N_8585.contig-group-19.g.vcf.gz, called/N_8586.contig-group-19.g.vcf.gz, called/N_9104.contig-group-19.g.vcf.gz, called/N_9449.contig-group-19.g.vcf.gz, called/N_94.contig-group-19.g.vcf.gz, called/T1481.contig-group-19.g.vcf.gz, called/T1483.contig-group-19.g.vcf.gz, called/T178.contig-group-19.g.vcf.gz, called/T179.contig-group-19.g.vcf.gz, called/T180.contig-group-19.g.vcf.gz, called/T181.contig-group-19.g.vcf.gz, called/T185.contig-group-19.g.vcf.gz, called/T186.contig-group-19.g.vcf.gz, called/T187.contig-group-19.g.vcf.gz, called/T188.contig-group-19.g.vcf.gz, called/T189.contig-group-19.g.vcf.gz, called/T190.contig-group-19.g.vcf.gz, called/T192.contig-group-19.g.vcf.gz, called/T193.contig-group-19.g.vcf.gz, called/T194.contig-group-19.g.vcf.gz, called/T196.contig-group-19.g.vcf.gz, called/T248.contig-group-19.g.vcf.gz, called/T37.contig-group-19.g.vcf.gz, called/T72.contig-group-19.g.vcf.gz, called/T79.contig-group-19.g.vcf.gz, called/M1864_2.contig-group-19.g.vcf.gz.tbi, called/M1865_2.contig-group-19.g.vcf.gz.tbi, called/M5672.contig-group-19.g.vcf.gz.tbi, called/MTDC48361.contig-group-19.g.vcf.gz.tbi, called/N2005.contig-group-19.g.vcf.gz.tbi, called/N_102.contig-group-19.g.vcf.gz.tbi, called/N_1085.contig-group-19.g.vcf.gz.tbi, called/N_1156.contig-group-19.g.vcf.gz.tbi, called/N_1157.contig-group-19.g.vcf.gz.tbi, called/N_1158.contig-group-19.g.vcf.gz.tbi, called/N_1344.contig-group-19.g.vcf.gz.tbi, called/N_1347.contig-group-19.g.vcf.gz.tbi, called/N_1354.contig-group-19.g.vcf.gz.tbi, called/N_1355.contig-group-19.g.vcf.gz.tbi, called/N_1384.contig-group-19.g.vcf.gz.tbi, called/N_1386.contig-group-19.g.vcf.gz.tbi, called/N_1390.contig-group-19.g.vcf.gz.tbi, called/N_1409.contig-group-19.g.vcf.gz.tbi, called/N_1411.contig-group-19.g.vcf.gz.tbi, called/N_1413.contig-group-19.g.vcf.gz.tbi, called/N_1414.contig-group-19.g.vcf.gz.tbi, called/N_1609.contig-group-19.g.vcf.gz.tbi, called/N_1870.contig-group-19.g.vcf.gz.tbi, called/N_1901.contig-group-19.g.vcf.gz.tbi, called/N_1913.contig-group-19.g.vcf.gz.tbi, called/N_1927.contig-group-19.g.vcf.gz.tbi, called/N_192.contig-group-19.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-19.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-19.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-19.g.vcf.gz.tbi, called/N_1992_0123.contig-group-19.g.vcf.gz.tbi, called/N_1998_0130.contig-group-19.g.vcf.gz.tbi, called/N_2001_0025.contig-group-19.g.vcf.gz.tbi, called/N_2001_0205.contig-group-19.g.vcf.gz.tbi, called/N_2002_0292.contig-group-19.g.vcf.gz.tbi, called/N_2003_5409.contig-group-19.g.vcf.gz.tbi, called/N_2004.contig-group-19.g.vcf.gz.tbi, called/N_2010_1759.contig-group-19.g.vcf.gz.tbi, called/N_21.contig-group-19.g.vcf.gz.tbi, called/N_351.contig-group-19.g.vcf.gz.tbi, called/N_355.contig-group-19.g.vcf.gz.tbi, called/N_401.contig-group-19.g.vcf.gz.tbi, called/N_403.contig-group-19.g.vcf.gz.tbi, called/N_4843.contig-group-19.g.vcf.gz.tbi, called/N_4844.contig-group-19.g.vcf.gz.tbi, called/N_4846.contig-group-19.g.vcf.gz.tbi, called/N_4847.contig-group-19.g.vcf.gz.tbi, called/N_5056.contig-group-19.g.vcf.gz.tbi, called/N_5057.contig-group-19.g.vcf.gz.tbi, called/N_5129.contig-group-19.g.vcf.gz.tbi, called/N_6489.contig-group-19.g.vcf.gz.tbi, called/N_6490.contig-group-19.g.vcf.gz.tbi, called/N_685.contig-group-19.g.vcf.gz.tbi, called/N_689.contig-group-19.g.vcf.gz.tbi, called/N_690.contig-group-19.g.vcf.gz.tbi, called/N_6926.contig-group-19.g.vcf.gz.tbi, called/N_6928.contig-group-19.g.vcf.gz.tbi, called/N_6932.contig-group-19.g.vcf.gz.tbi, called/N_6.contig-group-19.g.vcf.gz.tbi, called/N_7083.contig-group-19.g.vcf.gz.tbi, called/N_79.contig-group-19.g.vcf.gz.tbi, called/N_7.contig-group-19.g.vcf.gz.tbi, called/N_8105.contig-group-19.g.vcf.gz.tbi, called/N_8171.contig-group-19.g.vcf.gz.tbi, called/N_83.contig-group-19.g.vcf.gz.tbi, called/N_8564.contig-group-19.g.vcf.gz.tbi, called/N_8565.contig-group-19.g.vcf.gz.tbi, called/N_8583.contig-group-19.g.vcf.gz.tbi, called/N_8585.contig-group-19.g.vcf.gz.tbi, called/N_8586.contig-group-19.g.vcf.gz.tbi, called/N_9104.contig-group-19.g.vcf.gz.tbi, called/N_9449.contig-group-19.g.vcf.gz.tbi, called/N_94.contig-group-19.g.vcf.gz.tbi, called/T1481.contig-group-19.g.vcf.gz.tbi, called/T1483.contig-group-19.g.vcf.gz.tbi, called/T178.contig-group-19.g.vcf.gz.tbi, called/T179.contig-group-19.g.vcf.gz.tbi, called/T180.contig-group-19.g.vcf.gz.tbi, called/T181.contig-group-19.g.vcf.gz.tbi, called/T185.contig-group-19.g.vcf.gz.tbi, called/T186.contig-group-19.g.vcf.gz.tbi, called/T187.contig-group-19.g.vcf.gz.tbi, called/T188.contig-group-19.g.vcf.gz.tbi, called/T189.contig-group-19.g.vcf.gz.tbi, called/T190.contig-group-19.g.vcf.gz.tbi, called/T192.contig-group-19.g.vcf.gz.tbi, called/T193.contig-group-19.g.vcf.gz.tbi, called/T194.contig-group-19.g.vcf.gz.tbi, called/T196.contig-group-19.g.vcf.gz.tbi, called/T248.contig-group-19.g.vcf.gz.tbi, called/T37.contig-group-19.g.vcf.gz.tbi, called/T72.contig-group-19.g.vcf.gz.tbi, called/T79.contig-group-19.g.vcf.gz.tbi output: called/all.contig-group-19.g.vcf.gz, called/all.contig-group-19.g.done log: logs/gatk/combine-gvcfs/contig-group-19.log jobid: 3229 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-19.bench.log reason: Input files updated by another job: called/N_6490.contig-group-19.g.vcf.gz.tbi, called/T185.contig-group-19.g.vcf.gz, called/N_4847.contig-group-19.g.vcf.gz, called/N_1157.contig-group-19.g.vcf.gz.tbi, called/N_1354.contig-group-19.g.vcf.gz, called/T72.contig-group-19.g.vcf.gz, called/T79.contig-group-19.g.vcf.gz, called/N_83.contig-group-19.g.vcf.gz.tbi, called/N_1158.contig-group-19.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-19.g.vcf.gz.tbi, called/N_690.contig-group-19.g.vcf.gz.tbi, called/T190.contig-group-19.g.vcf.gz.tbi, called/N_6928.contig-group-19.g.vcf.gz, called/N_6928.contig-group-19.g.vcf.gz.tbi, called/N_1992_0123.contig-group-19.g.vcf.gz, called/T180.contig-group-19.g.vcf.gz.tbi, called/N_8565.contig-group-19.g.vcf.gz.tbi, called/N_1992_0123.contig-group-19.g.vcf.gz.tbi, called/N2005.contig-group-19.g.vcf.gz.tbi, called/N_689.contig-group-19.g.vcf.gz, called/N_83.contig-group-19.g.vcf.gz, called/N_8583.contig-group-19.g.vcf.gz, called/N_351.contig-group-19.g.vcf.gz, called/N_1609.contig-group-19.g.vcf.gz.tbi, called/T1483.contig-group-19.g.vcf.gz.tbi, called/N_5129.contig-group-19.g.vcf.gz, called/N_79.contig-group-19.g.vcf.gz, called/N_2003_5409.contig-group-19.g.vcf.gz, called/N2005.contig-group-19.g.vcf.gz, called/N_4847.contig-group-19.g.vcf.gz.tbi, called/T190.contig-group-19.g.vcf.gz, called/T185.contig-group-19.g.vcf.gz.tbi, called/N_8565.contig-group-19.g.vcf.gz, called/T196.contig-group-19.g.vcf.gz, called/T192.contig-group-19.g.vcf.gz.tbi, called/M5672.contig-group-19.g.vcf.gz, called/T180.contig-group-19.g.vcf.gz, called/N_8583.contig-group-19.g.vcf.gz.tbi, called/N_2003_5409.contig-group-19.g.vcf.gz.tbi, called/N_8171.contig-group-19.g.vcf.gz, called/T79.contig-group-19.g.vcf.gz.tbi, called/N_1158.contig-group-19.g.vcf.gz, called/T1483.contig-group-19.g.vcf.gz, called/N_1354.contig-group-19.g.vcf.gz.tbi, called/N_8171.contig-group-19.g.vcf.gz.tbi, called/N_690.contig-group-19.g.vcf.gz, called/N_9104.contig-group-19.g.vcf.gz.tbi, called/N_351.contig-group-19.g.vcf.gz.tbi, called/N_1870.contig-group-19.g.vcf.gz.tbi, called/T192.contig-group-19.g.vcf.gz, called/N_1156.contig-group-19.g.vcf.gz.tbi, called/N_6490.contig-group-19.g.vcf.gz, called/N_1386.contig-group-19.g.vcf.gz, called/T187.contig-group-19.g.vcf.gz.tbi, called/N_4843.contig-group-19.g.vcf.gz, called/N_9104.contig-group-19.g.vcf.gz, called/N_1927.contig-group-19.g.vcf.gz, called/N_79.contig-group-19.g.vcf.gz.tbi, called/N_102.contig-group-19.g.vcf.gz, called/N_1157.contig-group-19.g.vcf.gz, called/N_6489.contig-group-19.g.vcf.gz, called/N_1927.contig-group-19.g.vcf.gz.tbi, called/N_1156.contig-group-19.g.vcf.gz, called/N_9449.contig-group-19.g.vcf.gz, called/T72.contig-group-19.g.vcf.gz.tbi, called/N_1386.contig-group-19.g.vcf.gz.tbi, called/N_1609.contig-group-19.g.vcf.gz, called/N_1870.contig-group-19.g.vcf.gz, called/N_6489.contig-group-19.g.vcf.gz.tbi, called/M5672.contig-group-19.g.vcf.gz.tbi, called/T187.contig-group-19.g.vcf.gz, called/N_4843.contig-group-19.g.vcf.gz.tbi, called/T196.contig-group-19.g.vcf.gz.tbi, called/N_102.contig-group-19.g.vcf.gz.tbi, called/N_689.contig-group-19.g.vcf.gz.tbi, called/N_9449.contig-group-19.g.vcf.gz.tbi, called/N_5129.contig-group-19.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-19.g.vcf.gz wildcards: contig=contig-group-19 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-1.g.vcf.gz, called/M1865_2.contig-group-1.g.vcf.gz, called/M5672.contig-group-1.g.vcf.gz, called/MTDC48361.contig-group-1.g.vcf.gz, called/N2005.contig-group-1.g.vcf.gz, called/N_102.contig-group-1.g.vcf.gz, called/N_1085.contig-group-1.g.vcf.gz, called/N_1156.contig-group-1.g.vcf.gz, called/N_1157.contig-group-1.g.vcf.gz, called/N_1158.contig-group-1.g.vcf.gz, called/N_1344.contig-group-1.g.vcf.gz, called/N_1347.contig-group-1.g.vcf.gz, called/N_1354.contig-group-1.g.vcf.gz, called/N_1355.contig-group-1.g.vcf.gz, called/N_1384.contig-group-1.g.vcf.gz, called/N_1386.contig-group-1.g.vcf.gz, called/N_1390.contig-group-1.g.vcf.gz, called/N_1409.contig-group-1.g.vcf.gz, called/N_1411.contig-group-1.g.vcf.gz, called/N_1413.contig-group-1.g.vcf.gz, called/N_1414.contig-group-1.g.vcf.gz, called/N_1609.contig-group-1.g.vcf.gz, called/N_1870.contig-group-1.g.vcf.gz, called/N_1901.contig-group-1.g.vcf.gz, called/N_1913.contig-group-1.g.vcf.gz, called/N_1927.contig-group-1.g.vcf.gz, called/N_192.contig-group-1.g.vcf.gz, called/N_1934_1_1_368.contig-group-1.g.vcf.gz, called/N_1934_1_1_5973.contig-group-1.g.vcf.gz, called/N_1951_13_1951.contig-group-1.g.vcf.gz, called/N_1992_0123.contig-group-1.g.vcf.gz, called/N_1998_0130.contig-group-1.g.vcf.gz, called/N_2001_0025.contig-group-1.g.vcf.gz, called/N_2001_0205.contig-group-1.g.vcf.gz, called/N_2002_0292.contig-group-1.g.vcf.gz, called/N_2003_5409.contig-group-1.g.vcf.gz, called/N_2004.contig-group-1.g.vcf.gz, called/N_2010_1759.contig-group-1.g.vcf.gz, called/N_21.contig-group-1.g.vcf.gz, called/N_351.contig-group-1.g.vcf.gz, called/N_355.contig-group-1.g.vcf.gz, called/N_401.contig-group-1.g.vcf.gz, called/N_403.contig-group-1.g.vcf.gz, called/N_4843.contig-group-1.g.vcf.gz, called/N_4844.contig-group-1.g.vcf.gz, called/N_4846.contig-group-1.g.vcf.gz, called/N_4847.contig-group-1.g.vcf.gz, called/N_5056.contig-group-1.g.vcf.gz, called/N_5057.contig-group-1.g.vcf.gz, called/N_5129.contig-group-1.g.vcf.gz, called/N_6489.contig-group-1.g.vcf.gz, called/N_6490.contig-group-1.g.vcf.gz, called/N_685.contig-group-1.g.vcf.gz, called/N_689.contig-group-1.g.vcf.gz, called/N_690.contig-group-1.g.vcf.gz, called/N_6926.contig-group-1.g.vcf.gz, called/N_6928.contig-group-1.g.vcf.gz, called/N_6932.contig-group-1.g.vcf.gz, called/N_6.contig-group-1.g.vcf.gz, called/N_7083.contig-group-1.g.vcf.gz, called/N_79.contig-group-1.g.vcf.gz, called/N_7.contig-group-1.g.vcf.gz, called/N_8105.contig-group-1.g.vcf.gz, called/N_8171.contig-group-1.g.vcf.gz, called/N_83.contig-group-1.g.vcf.gz, called/N_8564.contig-group-1.g.vcf.gz, called/N_8565.contig-group-1.g.vcf.gz, called/N_8583.contig-group-1.g.vcf.gz, called/N_8585.contig-group-1.g.vcf.gz, called/N_8586.contig-group-1.g.vcf.gz, called/N_9104.contig-group-1.g.vcf.gz, called/N_9449.contig-group-1.g.vcf.gz, called/N_94.contig-group-1.g.vcf.gz, called/T1481.contig-group-1.g.vcf.gz, called/T1483.contig-group-1.g.vcf.gz, called/T178.contig-group-1.g.vcf.gz, called/T179.contig-group-1.g.vcf.gz, called/T180.contig-group-1.g.vcf.gz, called/T181.contig-group-1.g.vcf.gz, called/T185.contig-group-1.g.vcf.gz, called/T186.contig-group-1.g.vcf.gz, called/T187.contig-group-1.g.vcf.gz, called/T188.contig-group-1.g.vcf.gz, called/T189.contig-group-1.g.vcf.gz, called/T190.contig-group-1.g.vcf.gz, called/T192.contig-group-1.g.vcf.gz, called/T193.contig-group-1.g.vcf.gz, called/T194.contig-group-1.g.vcf.gz, called/T196.contig-group-1.g.vcf.gz, called/T248.contig-group-1.g.vcf.gz, called/T37.contig-group-1.g.vcf.gz, called/T72.contig-group-1.g.vcf.gz, called/T79.contig-group-1.g.vcf.gz, called/M1864_2.contig-group-1.g.vcf.gz.tbi, called/M1865_2.contig-group-1.g.vcf.gz.tbi, called/M5672.contig-group-1.g.vcf.gz.tbi, called/MTDC48361.contig-group-1.g.vcf.gz.tbi, called/N2005.contig-group-1.g.vcf.gz.tbi, called/N_102.contig-group-1.g.vcf.gz.tbi, called/N_1085.contig-group-1.g.vcf.gz.tbi, called/N_1156.contig-group-1.g.vcf.gz.tbi, called/N_1157.contig-group-1.g.vcf.gz.tbi, called/N_1158.contig-group-1.g.vcf.gz.tbi, called/N_1344.contig-group-1.g.vcf.gz.tbi, called/N_1347.contig-group-1.g.vcf.gz.tbi, called/N_1354.contig-group-1.g.vcf.gz.tbi, called/N_1355.contig-group-1.g.vcf.gz.tbi, called/N_1384.contig-group-1.g.vcf.gz.tbi, called/N_1386.contig-group-1.g.vcf.gz.tbi, called/N_1390.contig-group-1.g.vcf.gz.tbi, called/N_1409.contig-group-1.g.vcf.gz.tbi, called/N_1411.contig-group-1.g.vcf.gz.tbi, called/N_1413.contig-group-1.g.vcf.gz.tbi, called/N_1414.contig-group-1.g.vcf.gz.tbi, called/N_1609.contig-group-1.g.vcf.gz.tbi, called/N_1870.contig-group-1.g.vcf.gz.tbi, called/N_1901.contig-group-1.g.vcf.gz.tbi, called/N_1913.contig-group-1.g.vcf.gz.tbi, called/N_1927.contig-group-1.g.vcf.gz.tbi, called/N_192.contig-group-1.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-1.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-1.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-1.g.vcf.gz.tbi, called/N_1992_0123.contig-group-1.g.vcf.gz.tbi, called/N_1998_0130.contig-group-1.g.vcf.gz.tbi, called/N_2001_0025.contig-group-1.g.vcf.gz.tbi, called/N_2001_0205.contig-group-1.g.vcf.gz.tbi, called/N_2002_0292.contig-group-1.g.vcf.gz.tbi, called/N_2003_5409.contig-group-1.g.vcf.gz.tbi, called/N_2004.contig-group-1.g.vcf.gz.tbi, called/N_2010_1759.contig-group-1.g.vcf.gz.tbi, called/N_21.contig-group-1.g.vcf.gz.tbi, called/N_351.contig-group-1.g.vcf.gz.tbi, called/N_355.contig-group-1.g.vcf.gz.tbi, called/N_401.contig-group-1.g.vcf.gz.tbi, called/N_403.contig-group-1.g.vcf.gz.tbi, called/N_4843.contig-group-1.g.vcf.gz.tbi, called/N_4844.contig-group-1.g.vcf.gz.tbi, called/N_4846.contig-group-1.g.vcf.gz.tbi, called/N_4847.contig-group-1.g.vcf.gz.tbi, called/N_5056.contig-group-1.g.vcf.gz.tbi, called/N_5057.contig-group-1.g.vcf.gz.tbi, called/N_5129.contig-group-1.g.vcf.gz.tbi, called/N_6489.contig-group-1.g.vcf.gz.tbi, called/N_6490.contig-group-1.g.vcf.gz.tbi, called/N_685.contig-group-1.g.vcf.gz.tbi, called/N_689.contig-group-1.g.vcf.gz.tbi, called/N_690.contig-group-1.g.vcf.gz.tbi, called/N_6926.contig-group-1.g.vcf.gz.tbi, called/N_6928.contig-group-1.g.vcf.gz.tbi, called/N_6932.contig-group-1.g.vcf.gz.tbi, called/N_6.contig-group-1.g.vcf.gz.tbi, called/N_7083.contig-group-1.g.vcf.gz.tbi, called/N_79.contig-group-1.g.vcf.gz.tbi, called/N_7.contig-group-1.g.vcf.gz.tbi, called/N_8105.contig-group-1.g.vcf.gz.tbi, called/N_8171.contig-group-1.g.vcf.gz.tbi, called/N_83.contig-group-1.g.vcf.gz.tbi, called/N_8564.contig-group-1.g.vcf.gz.tbi, called/N_8565.contig-group-1.g.vcf.gz.tbi, called/N_8583.contig-group-1.g.vcf.gz.tbi, called/N_8585.contig-group-1.g.vcf.gz.tbi, called/N_8586.contig-group-1.g.vcf.gz.tbi, called/N_9104.contig-group-1.g.vcf.gz.tbi, called/N_9449.contig-group-1.g.vcf.gz.tbi, called/N_94.contig-group-1.g.vcf.gz.tbi, called/T1481.contig-group-1.g.vcf.gz.tbi, called/T1483.contig-group-1.g.vcf.gz.tbi, called/T178.contig-group-1.g.vcf.gz.tbi, called/T179.contig-group-1.g.vcf.gz.tbi, called/T180.contig-group-1.g.vcf.gz.tbi, called/T181.contig-group-1.g.vcf.gz.tbi, called/T185.contig-group-1.g.vcf.gz.tbi, called/T186.contig-group-1.g.vcf.gz.tbi, called/T187.contig-group-1.g.vcf.gz.tbi, called/T188.contig-group-1.g.vcf.gz.tbi, called/T189.contig-group-1.g.vcf.gz.tbi, called/T190.contig-group-1.g.vcf.gz.tbi, called/T192.contig-group-1.g.vcf.gz.tbi, called/T193.contig-group-1.g.vcf.gz.tbi, called/T194.contig-group-1.g.vcf.gz.tbi, called/T196.contig-group-1.g.vcf.gz.tbi, called/T248.contig-group-1.g.vcf.gz.tbi, called/T37.contig-group-1.g.vcf.gz.tbi, called/T72.contig-group-1.g.vcf.gz.tbi, called/T79.contig-group-1.g.vcf.gz.tbi output: called/all.contig-group-1.g.vcf.gz, called/all.contig-group-1.g.done log: logs/gatk/combine-gvcfs/contig-group-1.log jobid: 1501 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-1.bench.log reason: Input files updated by another job: called/T196.contig-group-1.g.vcf.gz.tbi, called/N_79.contig-group-1.g.vcf.gz, called/T185.contig-group-1.g.vcf.gz, called/T187.contig-group-1.g.vcf.gz, called/N2005.contig-group-1.g.vcf.gz.tbi, called/N_8171.contig-group-1.g.vcf.gz.tbi, called/N_8583.contig-group-1.g.vcf.gz.tbi, called/T79.contig-group-1.g.vcf.gz.tbi, called/N_1386.contig-group-1.g.vcf.gz, called/T196.contig-group-1.g.vcf.gz, called/N_351.contig-group-1.g.vcf.gz, called/M5672.contig-group-1.g.vcf.gz.tbi, called/T190.contig-group-1.g.vcf.gz.tbi, called/N_102.contig-group-1.g.vcf.gz.tbi, called/T185.contig-group-1.g.vcf.gz.tbi, called/N_1609.contig-group-1.g.vcf.gz.tbi, called/N_8583.contig-group-1.g.vcf.gz, called/N_1934_1_1_5973.contig-group-1.g.vcf.gz, called/T180.contig-group-1.g.vcf.gz.tbi, called/N_689.contig-group-1.g.vcf.gz, called/M5672.contig-group-1.g.vcf.gz, called/N_1158.contig-group-1.g.vcf.gz.tbi, called/N_5129.contig-group-1.g.vcf.gz.tbi, called/N_1156.contig-group-1.g.vcf.gz.tbi, called/N_9104.contig-group-1.g.vcf.gz.tbi, called/N_8171.contig-group-1.g.vcf.gz, called/N_1157.contig-group-1.g.vcf.gz.tbi, called/N_6489.contig-group-1.g.vcf.gz.tbi, called/N_2003_5409.contig-group-1.g.vcf.gz, called/N_1992_0123.contig-group-1.g.vcf.gz, called/T1483.contig-group-1.g.vcf.gz.tbi, called/T190.contig-group-1.g.vcf.gz, called/N_6928.contig-group-1.g.vcf.gz, called/N_79.contig-group-1.g.vcf.gz.tbi, called/T72.contig-group-1.g.vcf.gz.tbi, called/N_1156.contig-group-1.g.vcf.gz, called/N_102.contig-group-1.g.vcf.gz, called/N_1870.contig-group-1.g.vcf.gz, called/N_4847.contig-group-1.g.vcf.gz.tbi, called/N_9449.contig-group-1.g.vcf.gz.tbi, called/N_1870.contig-group-1.g.vcf.gz.tbi, called/T187.contig-group-1.g.vcf.gz.tbi, called/T79.contig-group-1.g.vcf.gz, called/N_83.contig-group-1.g.vcf.gz, called/N_5129.contig-group-1.g.vcf.gz, called/N_6489.contig-group-1.g.vcf.gz, called/N_1927.contig-group-1.g.vcf.gz.tbi, called/N_1354.contig-group-1.g.vcf.gz, called/N_1992_0123.contig-group-1.g.vcf.gz.tbi, called/N_1354.contig-group-1.g.vcf.gz.tbi, called/N_8565.contig-group-1.g.vcf.gz, called/T72.contig-group-1.g.vcf.gz, called/T192.contig-group-1.g.vcf.gz.tbi, called/N_351.contig-group-1.g.vcf.gz.tbi, called/N_1609.contig-group-1.g.vcf.gz, called/N_4847.contig-group-1.g.vcf.gz, called/N_4843.contig-group-1.g.vcf.gz.tbi, called/T192.contig-group-1.g.vcf.gz, called/N_4843.contig-group-1.g.vcf.gz, called/N_1158.contig-group-1.g.vcf.gz, called/N_1157.contig-group-1.g.vcf.gz, called/N_1934_1_1_5973.contig-group-1.g.vcf.gz.tbi, called/N_6928.contig-group-1.g.vcf.gz.tbi, called/N_689.contig-group-1.g.vcf.gz.tbi, called/N_690.contig-group-1.g.vcf.gz.tbi, called/N_8565.contig-group-1.g.vcf.gz.tbi, called/N_6490.contig-group-1.g.vcf.gz, called/N2005.contig-group-1.g.vcf.gz, called/T1483.contig-group-1.g.vcf.gz, called/N_83.contig-group-1.g.vcf.gz.tbi, called/T180.contig-group-1.g.vcf.gz, called/N_9104.contig-group-1.g.vcf.gz, called/N_9449.contig-group-1.g.vcf.gz, called/N_2003_5409.contig-group-1.g.vcf.gz.tbi, called/N_690.contig-group-1.g.vcf.gz, called/N_1386.contig-group-1.g.vcf.gz.tbi, called/N_1927.contig-group-1.g.vcf.gz, called/N_6490.contig-group-1.g.vcf.gz.tbi wildcards: contig=contig-group-1 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-7.g.vcf.gz, called/M1865_2.contig-group-7.g.vcf.gz, called/M5672.contig-group-7.g.vcf.gz, called/MTDC48361.contig-group-7.g.vcf.gz, called/N2005.contig-group-7.g.vcf.gz, called/N_102.contig-group-7.g.vcf.gz, called/N_1085.contig-group-7.g.vcf.gz, called/N_1156.contig-group-7.g.vcf.gz, called/N_1157.contig-group-7.g.vcf.gz, called/N_1158.contig-group-7.g.vcf.gz, called/N_1344.contig-group-7.g.vcf.gz, called/N_1347.contig-group-7.g.vcf.gz, called/N_1354.contig-group-7.g.vcf.gz, called/N_1355.contig-group-7.g.vcf.gz, called/N_1384.contig-group-7.g.vcf.gz, called/N_1386.contig-group-7.g.vcf.gz, called/N_1390.contig-group-7.g.vcf.gz, called/N_1409.contig-group-7.g.vcf.gz, called/N_1411.contig-group-7.g.vcf.gz, called/N_1413.contig-group-7.g.vcf.gz, called/N_1414.contig-group-7.g.vcf.gz, called/N_1609.contig-group-7.g.vcf.gz, called/N_1870.contig-group-7.g.vcf.gz, called/N_1901.contig-group-7.g.vcf.gz, called/N_1913.contig-group-7.g.vcf.gz, called/N_1927.contig-group-7.g.vcf.gz, called/N_192.contig-group-7.g.vcf.gz, called/N_1934_1_1_368.contig-group-7.g.vcf.gz, called/N_1934_1_1_5973.contig-group-7.g.vcf.gz, called/N_1951_13_1951.contig-group-7.g.vcf.gz, called/N_1992_0123.contig-group-7.g.vcf.gz, called/N_1998_0130.contig-group-7.g.vcf.gz, called/N_2001_0025.contig-group-7.g.vcf.gz, called/N_2001_0205.contig-group-7.g.vcf.gz, called/N_2002_0292.contig-group-7.g.vcf.gz, called/N_2003_5409.contig-group-7.g.vcf.gz, called/N_2004.contig-group-7.g.vcf.gz, called/N_2010_1759.contig-group-7.g.vcf.gz, called/N_21.contig-group-7.g.vcf.gz, called/N_351.contig-group-7.g.vcf.gz, called/N_355.contig-group-7.g.vcf.gz, called/N_401.contig-group-7.g.vcf.gz, called/N_403.contig-group-7.g.vcf.gz, called/N_4843.contig-group-7.g.vcf.gz, called/N_4844.contig-group-7.g.vcf.gz, called/N_4846.contig-group-7.g.vcf.gz, called/N_4847.contig-group-7.g.vcf.gz, called/N_5056.contig-group-7.g.vcf.gz, called/N_5057.contig-group-7.g.vcf.gz, called/N_5129.contig-group-7.g.vcf.gz, called/N_6489.contig-group-7.g.vcf.gz, called/N_6490.contig-group-7.g.vcf.gz, called/N_685.contig-group-7.g.vcf.gz, called/N_689.contig-group-7.g.vcf.gz, called/N_690.contig-group-7.g.vcf.gz, called/N_6926.contig-group-7.g.vcf.gz, called/N_6928.contig-group-7.g.vcf.gz, called/N_6932.contig-group-7.g.vcf.gz, called/N_6.contig-group-7.g.vcf.gz, called/N_7083.contig-group-7.g.vcf.gz, called/N_79.contig-group-7.g.vcf.gz, called/N_7.contig-group-7.g.vcf.gz, called/N_8105.contig-group-7.g.vcf.gz, called/N_8171.contig-group-7.g.vcf.gz, called/N_83.contig-group-7.g.vcf.gz, called/N_8564.contig-group-7.g.vcf.gz, called/N_8565.contig-group-7.g.vcf.gz, called/N_8583.contig-group-7.g.vcf.gz, called/N_8585.contig-group-7.g.vcf.gz, called/N_8586.contig-group-7.g.vcf.gz, called/N_9104.contig-group-7.g.vcf.gz, called/N_9449.contig-group-7.g.vcf.gz, called/N_94.contig-group-7.g.vcf.gz, called/T1481.contig-group-7.g.vcf.gz, called/T1483.contig-group-7.g.vcf.gz, called/T178.contig-group-7.g.vcf.gz, called/T179.contig-group-7.g.vcf.gz, called/T180.contig-group-7.g.vcf.gz, called/T181.contig-group-7.g.vcf.gz, called/T185.contig-group-7.g.vcf.gz, called/T186.contig-group-7.g.vcf.gz, called/T187.contig-group-7.g.vcf.gz, called/T188.contig-group-7.g.vcf.gz, called/T189.contig-group-7.g.vcf.gz, called/T190.contig-group-7.g.vcf.gz, called/T192.contig-group-7.g.vcf.gz, called/T193.contig-group-7.g.vcf.gz, called/T194.contig-group-7.g.vcf.gz, called/T196.contig-group-7.g.vcf.gz, called/T248.contig-group-7.g.vcf.gz, called/T37.contig-group-7.g.vcf.gz, called/T72.contig-group-7.g.vcf.gz, called/T79.contig-group-7.g.vcf.gz, called/M1864_2.contig-group-7.g.vcf.gz.tbi, called/M1865_2.contig-group-7.g.vcf.gz.tbi, called/M5672.contig-group-7.g.vcf.gz.tbi, called/MTDC48361.contig-group-7.g.vcf.gz.tbi, called/N2005.contig-group-7.g.vcf.gz.tbi, called/N_102.contig-group-7.g.vcf.gz.tbi, called/N_1085.contig-group-7.g.vcf.gz.tbi, called/N_1156.contig-group-7.g.vcf.gz.tbi, called/N_1157.contig-group-7.g.vcf.gz.tbi, called/N_1158.contig-group-7.g.vcf.gz.tbi, called/N_1344.contig-group-7.g.vcf.gz.tbi, called/N_1347.contig-group-7.g.vcf.gz.tbi, called/N_1354.contig-group-7.g.vcf.gz.tbi, called/N_1355.contig-group-7.g.vcf.gz.tbi, called/N_1384.contig-group-7.g.vcf.gz.tbi, called/N_1386.contig-group-7.g.vcf.gz.tbi, called/N_1390.contig-group-7.g.vcf.gz.tbi, called/N_1409.contig-group-7.g.vcf.gz.tbi, called/N_1411.contig-group-7.g.vcf.gz.tbi, called/N_1413.contig-group-7.g.vcf.gz.tbi, called/N_1414.contig-group-7.g.vcf.gz.tbi, called/N_1609.contig-group-7.g.vcf.gz.tbi, called/N_1870.contig-group-7.g.vcf.gz.tbi, called/N_1901.contig-group-7.g.vcf.gz.tbi, called/N_1913.contig-group-7.g.vcf.gz.tbi, called/N_1927.contig-group-7.g.vcf.gz.tbi, called/N_192.contig-group-7.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-7.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-7.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-7.g.vcf.gz.tbi, called/N_1992_0123.contig-group-7.g.vcf.gz.tbi, called/N_1998_0130.contig-group-7.g.vcf.gz.tbi, called/N_2001_0025.contig-group-7.g.vcf.gz.tbi, called/N_2001_0205.contig-group-7.g.vcf.gz.tbi, called/N_2002_0292.contig-group-7.g.vcf.gz.tbi, called/N_2003_5409.contig-group-7.g.vcf.gz.tbi, called/N_2004.contig-group-7.g.vcf.gz.tbi, called/N_2010_1759.contig-group-7.g.vcf.gz.tbi, called/N_21.contig-group-7.g.vcf.gz.tbi, called/N_351.contig-group-7.g.vcf.gz.tbi, called/N_355.contig-group-7.g.vcf.gz.tbi, called/N_401.contig-group-7.g.vcf.gz.tbi, called/N_403.contig-group-7.g.vcf.gz.tbi, called/N_4843.contig-group-7.g.vcf.gz.tbi, called/N_4844.contig-group-7.g.vcf.gz.tbi, called/N_4846.contig-group-7.g.vcf.gz.tbi, called/N_4847.contig-group-7.g.vcf.gz.tbi, called/N_5056.contig-group-7.g.vcf.gz.tbi, called/N_5057.contig-group-7.g.vcf.gz.tbi, called/N_5129.contig-group-7.g.vcf.gz.tbi, called/N_6489.contig-group-7.g.vcf.gz.tbi, called/N_6490.contig-group-7.g.vcf.gz.tbi, called/N_685.contig-group-7.g.vcf.gz.tbi, called/N_689.contig-group-7.g.vcf.gz.tbi, called/N_690.contig-group-7.g.vcf.gz.tbi, called/N_6926.contig-group-7.g.vcf.gz.tbi, called/N_6928.contig-group-7.g.vcf.gz.tbi, called/N_6932.contig-group-7.g.vcf.gz.tbi, called/N_6.contig-group-7.g.vcf.gz.tbi, called/N_7083.contig-group-7.g.vcf.gz.tbi, called/N_79.contig-group-7.g.vcf.gz.tbi, called/N_7.contig-group-7.g.vcf.gz.tbi, called/N_8105.contig-group-7.g.vcf.gz.tbi, called/N_8171.contig-group-7.g.vcf.gz.tbi, called/N_83.contig-group-7.g.vcf.gz.tbi, called/N_8564.contig-group-7.g.vcf.gz.tbi, called/N_8565.contig-group-7.g.vcf.gz.tbi, called/N_8583.contig-group-7.g.vcf.gz.tbi, called/N_8585.contig-group-7.g.vcf.gz.tbi, called/N_8586.contig-group-7.g.vcf.gz.tbi, called/N_9104.contig-group-7.g.vcf.gz.tbi, called/N_9449.contig-group-7.g.vcf.gz.tbi, called/N_94.contig-group-7.g.vcf.gz.tbi, called/T1481.contig-group-7.g.vcf.gz.tbi, called/T1483.contig-group-7.g.vcf.gz.tbi, called/T178.contig-group-7.g.vcf.gz.tbi, called/T179.contig-group-7.g.vcf.gz.tbi, called/T180.contig-group-7.g.vcf.gz.tbi, called/T181.contig-group-7.g.vcf.gz.tbi, called/T185.contig-group-7.g.vcf.gz.tbi, called/T186.contig-group-7.g.vcf.gz.tbi, called/T187.contig-group-7.g.vcf.gz.tbi, called/T188.contig-group-7.g.vcf.gz.tbi, called/T189.contig-group-7.g.vcf.gz.tbi, called/T190.contig-group-7.g.vcf.gz.tbi, called/T192.contig-group-7.g.vcf.gz.tbi, called/T193.contig-group-7.g.vcf.gz.tbi, called/T194.contig-group-7.g.vcf.gz.tbi, called/T196.contig-group-7.g.vcf.gz.tbi, called/T248.contig-group-7.g.vcf.gz.tbi, called/T37.contig-group-7.g.vcf.gz.tbi, called/T72.contig-group-7.g.vcf.gz.tbi, called/T79.contig-group-7.g.vcf.gz.tbi output: called/all.contig-group-7.g.vcf.gz, called/all.contig-group-7.g.done log: logs/gatk/combine-gvcfs/contig-group-7.log jobid: 2077 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-7.bench.log reason: Input files updated by another job: called/N_6489.contig-group-7.g.vcf.gz.tbi, called/N_1354.contig-group-7.g.vcf.gz, called/N_6489.contig-group-7.g.vcf.gz, called/N_1609.contig-group-7.g.vcf.gz, called/N_8565.contig-group-7.g.vcf.gz.tbi, called/T187.contig-group-7.g.vcf.gz, called/N_6490.contig-group-7.g.vcf.gz.tbi, called/N_690.contig-group-7.g.vcf.gz.tbi, called/N_9104.contig-group-7.g.vcf.gz, called/N_9104.contig-group-7.g.vcf.gz.tbi, called/M5672.contig-group-7.g.vcf.gz.tbi, called/N_79.contig-group-7.g.vcf.gz.tbi, called/N_83.contig-group-7.g.vcf.gz, called/T190.contig-group-7.g.vcf.gz, called/N_4843.contig-group-7.g.vcf.gz.tbi, called/N_1156.contig-group-7.g.vcf.gz, called/T190.contig-group-7.g.vcf.gz.tbi, called/N_1927.contig-group-7.g.vcf.gz, called/N_79.contig-group-7.g.vcf.gz, called/N_1609.contig-group-7.g.vcf.gz.tbi, called/N_8583.contig-group-7.g.vcf.gz, called/T196.contig-group-7.g.vcf.gz.tbi, called/T72.contig-group-7.g.vcf.gz, called/T1483.contig-group-7.g.vcf.gz.tbi, called/T192.contig-group-7.g.vcf.gz.tbi, called/N_5129.contig-group-7.g.vcf.gz.tbi, called/M5672.contig-group-7.g.vcf.gz, called/N_5129.contig-group-7.g.vcf.gz, called/T72.contig-group-7.g.vcf.gz.tbi, called/T79.contig-group-7.g.vcf.gz, called/T180.contig-group-7.g.vcf.gz, called/T196.contig-group-7.g.vcf.gz, called/N_1870.contig-group-7.g.vcf.gz, called/N_2003_5409.contig-group-7.g.vcf.gz.tbi, called/N_6928.contig-group-7.g.vcf.gz, called/N_1158.contig-group-7.g.vcf.gz, called/T1483.contig-group-7.g.vcf.gz, called/N_351.contig-group-7.g.vcf.gz, called/N_351.contig-group-7.g.vcf.gz.tbi, called/N_690.contig-group-7.g.vcf.gz, called/N_8583.contig-group-7.g.vcf.gz.tbi, called/T180.contig-group-7.g.vcf.gz.tbi, called/N_4847.contig-group-7.g.vcf.gz.tbi, called/T192.contig-group-7.g.vcf.gz, called/N_1158.contig-group-7.g.vcf.gz.tbi, called/N_9449.contig-group-7.g.vcf.gz, called/N_1992_0123.contig-group-7.g.vcf.gz.tbi, called/N2005.contig-group-7.g.vcf.gz, called/N_689.contig-group-7.g.vcf.gz.tbi, called/N_1992_0123.contig-group-7.g.vcf.gz, called/T185.contig-group-7.g.vcf.gz, called/N_1157.contig-group-7.g.vcf.gz.tbi, called/N_4847.contig-group-7.g.vcf.gz, called/N2005.contig-group-7.g.vcf.gz.tbi, called/N_1354.contig-group-7.g.vcf.gz.tbi, called/N_4843.contig-group-7.g.vcf.gz, called/N_1934_1_1_5973.contig-group-7.g.vcf.gz.tbi, called/N_6928.contig-group-7.g.vcf.gz.tbi, called/N_8565.contig-group-7.g.vcf.gz, called/N_689.contig-group-7.g.vcf.gz, called/N_1386.contig-group-7.g.vcf.gz.tbi, called/N_1870.contig-group-7.g.vcf.gz.tbi, called/N_1156.contig-group-7.g.vcf.gz.tbi, called/N_83.contig-group-7.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-7.g.vcf.gz, called/T79.contig-group-7.g.vcf.gz.tbi, called/N_102.contig-group-7.g.vcf.gz.tbi, called/N_1927.contig-group-7.g.vcf.gz.tbi, called/N_2003_5409.contig-group-7.g.vcf.gz, called/N_6490.contig-group-7.g.vcf.gz, called/T185.contig-group-7.g.vcf.gz.tbi, called/N_9449.contig-group-7.g.vcf.gz.tbi, called/T187.contig-group-7.g.vcf.gz.tbi, called/N_8171.contig-group-7.g.vcf.gz.tbi, called/N_102.contig-group-7.g.vcf.gz, called/N_8171.contig-group-7.g.vcf.gz, called/N_1386.contig-group-7.g.vcf.gz, called/N_1157.contig-group-7.g.vcf.gz wildcards: contig=contig-group-7 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-13.g.vcf.gz, called/M1865_2.contig-group-13.g.vcf.gz, called/M5672.contig-group-13.g.vcf.gz, called/MTDC48361.contig-group-13.g.vcf.gz, called/N2005.contig-group-13.g.vcf.gz, called/N_102.contig-group-13.g.vcf.gz, called/N_1085.contig-group-13.g.vcf.gz, called/N_1156.contig-group-13.g.vcf.gz, called/N_1157.contig-group-13.g.vcf.gz, called/N_1158.contig-group-13.g.vcf.gz, called/N_1344.contig-group-13.g.vcf.gz, called/N_1347.contig-group-13.g.vcf.gz, called/N_1354.contig-group-13.g.vcf.gz, called/N_1355.contig-group-13.g.vcf.gz, called/N_1384.contig-group-13.g.vcf.gz, called/N_1386.contig-group-13.g.vcf.gz, called/N_1390.contig-group-13.g.vcf.gz, called/N_1409.contig-group-13.g.vcf.gz, called/N_1411.contig-group-13.g.vcf.gz, called/N_1413.contig-group-13.g.vcf.gz, called/N_1414.contig-group-13.g.vcf.gz, called/N_1609.contig-group-13.g.vcf.gz, called/N_1870.contig-group-13.g.vcf.gz, called/N_1901.contig-group-13.g.vcf.gz, called/N_1913.contig-group-13.g.vcf.gz, called/N_1927.contig-group-13.g.vcf.gz, called/N_192.contig-group-13.g.vcf.gz, called/N_1934_1_1_368.contig-group-13.g.vcf.gz, called/N_1934_1_1_5973.contig-group-13.g.vcf.gz, called/N_1951_13_1951.contig-group-13.g.vcf.gz, called/N_1992_0123.contig-group-13.g.vcf.gz, called/N_1998_0130.contig-group-13.g.vcf.gz, called/N_2001_0025.contig-group-13.g.vcf.gz, called/N_2001_0205.contig-group-13.g.vcf.gz, called/N_2002_0292.contig-group-13.g.vcf.gz, called/N_2003_5409.contig-group-13.g.vcf.gz, called/N_2004.contig-group-13.g.vcf.gz, called/N_2010_1759.contig-group-13.g.vcf.gz, called/N_21.contig-group-13.g.vcf.gz, called/N_351.contig-group-13.g.vcf.gz, called/N_355.contig-group-13.g.vcf.gz, called/N_401.contig-group-13.g.vcf.gz, called/N_403.contig-group-13.g.vcf.gz, called/N_4843.contig-group-13.g.vcf.gz, called/N_4844.contig-group-13.g.vcf.gz, called/N_4846.contig-group-13.g.vcf.gz, called/N_4847.contig-group-13.g.vcf.gz, called/N_5056.contig-group-13.g.vcf.gz, called/N_5057.contig-group-13.g.vcf.gz, called/N_5129.contig-group-13.g.vcf.gz, called/N_6489.contig-group-13.g.vcf.gz, called/N_6490.contig-group-13.g.vcf.gz, called/N_685.contig-group-13.g.vcf.gz, called/N_689.contig-group-13.g.vcf.gz, called/N_690.contig-group-13.g.vcf.gz, called/N_6926.contig-group-13.g.vcf.gz, called/N_6928.contig-group-13.g.vcf.gz, called/N_6932.contig-group-13.g.vcf.gz, called/N_6.contig-group-13.g.vcf.gz, called/N_7083.contig-group-13.g.vcf.gz, called/N_79.contig-group-13.g.vcf.gz, called/N_7.contig-group-13.g.vcf.gz, called/N_8105.contig-group-13.g.vcf.gz, called/N_8171.contig-group-13.g.vcf.gz, called/N_83.contig-group-13.g.vcf.gz, called/N_8564.contig-group-13.g.vcf.gz, called/N_8565.contig-group-13.g.vcf.gz, called/N_8583.contig-group-13.g.vcf.gz, called/N_8585.contig-group-13.g.vcf.gz, called/N_8586.contig-group-13.g.vcf.gz, called/N_9104.contig-group-13.g.vcf.gz, called/N_9449.contig-group-13.g.vcf.gz, called/N_94.contig-group-13.g.vcf.gz, called/T1481.contig-group-13.g.vcf.gz, called/T1483.contig-group-13.g.vcf.gz, called/T178.contig-group-13.g.vcf.gz, called/T179.contig-group-13.g.vcf.gz, called/T180.contig-group-13.g.vcf.gz, called/T181.contig-group-13.g.vcf.gz, called/T185.contig-group-13.g.vcf.gz, called/T186.contig-group-13.g.vcf.gz, called/T187.contig-group-13.g.vcf.gz, called/T188.contig-group-13.g.vcf.gz, called/T189.contig-group-13.g.vcf.gz, called/T190.contig-group-13.g.vcf.gz, called/T192.contig-group-13.g.vcf.gz, called/T193.contig-group-13.g.vcf.gz, called/T194.contig-group-13.g.vcf.gz, called/T196.contig-group-13.g.vcf.gz, called/T248.contig-group-13.g.vcf.gz, called/T37.contig-group-13.g.vcf.gz, called/T72.contig-group-13.g.vcf.gz, called/T79.contig-group-13.g.vcf.gz, called/M1864_2.contig-group-13.g.vcf.gz.tbi, called/M1865_2.contig-group-13.g.vcf.gz.tbi, called/M5672.contig-group-13.g.vcf.gz.tbi, called/MTDC48361.contig-group-13.g.vcf.gz.tbi, called/N2005.contig-group-13.g.vcf.gz.tbi, called/N_102.contig-group-13.g.vcf.gz.tbi, called/N_1085.contig-group-13.g.vcf.gz.tbi, called/N_1156.contig-group-13.g.vcf.gz.tbi, called/N_1157.contig-group-13.g.vcf.gz.tbi, called/N_1158.contig-group-13.g.vcf.gz.tbi, called/N_1344.contig-group-13.g.vcf.gz.tbi, called/N_1347.contig-group-13.g.vcf.gz.tbi, called/N_1354.contig-group-13.g.vcf.gz.tbi, called/N_1355.contig-group-13.g.vcf.gz.tbi, called/N_1384.contig-group-13.g.vcf.gz.tbi, called/N_1386.contig-group-13.g.vcf.gz.tbi, called/N_1390.contig-group-13.g.vcf.gz.tbi, called/N_1409.contig-group-13.g.vcf.gz.tbi, called/N_1411.contig-group-13.g.vcf.gz.tbi, called/N_1413.contig-group-13.g.vcf.gz.tbi, called/N_1414.contig-group-13.g.vcf.gz.tbi, called/N_1609.contig-group-13.g.vcf.gz.tbi, called/N_1870.contig-group-13.g.vcf.gz.tbi, called/N_1901.contig-group-13.g.vcf.gz.tbi, called/N_1913.contig-group-13.g.vcf.gz.tbi, called/N_1927.contig-group-13.g.vcf.gz.tbi, called/N_192.contig-group-13.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-13.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-13.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-13.g.vcf.gz.tbi, called/N_1992_0123.contig-group-13.g.vcf.gz.tbi, called/N_1998_0130.contig-group-13.g.vcf.gz.tbi, called/N_2001_0025.contig-group-13.g.vcf.gz.tbi, called/N_2001_0205.contig-group-13.g.vcf.gz.tbi, called/N_2002_0292.contig-group-13.g.vcf.gz.tbi, called/N_2003_5409.contig-group-13.g.vcf.gz.tbi, called/N_2004.contig-group-13.g.vcf.gz.tbi, called/N_2010_1759.contig-group-13.g.vcf.gz.tbi, called/N_21.contig-group-13.g.vcf.gz.tbi, called/N_351.contig-group-13.g.vcf.gz.tbi, called/N_355.contig-group-13.g.vcf.gz.tbi, called/N_401.contig-group-13.g.vcf.gz.tbi, called/N_403.contig-group-13.g.vcf.gz.tbi, called/N_4843.contig-group-13.g.vcf.gz.tbi, called/N_4844.contig-group-13.g.vcf.gz.tbi, called/N_4846.contig-group-13.g.vcf.gz.tbi, called/N_4847.contig-group-13.g.vcf.gz.tbi, called/N_5056.contig-group-13.g.vcf.gz.tbi, called/N_5057.contig-group-13.g.vcf.gz.tbi, called/N_5129.contig-group-13.g.vcf.gz.tbi, called/N_6489.contig-group-13.g.vcf.gz.tbi, called/N_6490.contig-group-13.g.vcf.gz.tbi, called/N_685.contig-group-13.g.vcf.gz.tbi, called/N_689.contig-group-13.g.vcf.gz.tbi, called/N_690.contig-group-13.g.vcf.gz.tbi, called/N_6926.contig-group-13.g.vcf.gz.tbi, called/N_6928.contig-group-13.g.vcf.gz.tbi, called/N_6932.contig-group-13.g.vcf.gz.tbi, called/N_6.contig-group-13.g.vcf.gz.tbi, called/N_7083.contig-group-13.g.vcf.gz.tbi, called/N_79.contig-group-13.g.vcf.gz.tbi, called/N_7.contig-group-13.g.vcf.gz.tbi, called/N_8105.contig-group-13.g.vcf.gz.tbi, called/N_8171.contig-group-13.g.vcf.gz.tbi, called/N_83.contig-group-13.g.vcf.gz.tbi, called/N_8564.contig-group-13.g.vcf.gz.tbi, called/N_8565.contig-group-13.g.vcf.gz.tbi, called/N_8583.contig-group-13.g.vcf.gz.tbi, called/N_8585.contig-group-13.g.vcf.gz.tbi, called/N_8586.contig-group-13.g.vcf.gz.tbi, called/N_9104.contig-group-13.g.vcf.gz.tbi, called/N_9449.contig-group-13.g.vcf.gz.tbi, called/N_94.contig-group-13.g.vcf.gz.tbi, called/T1481.contig-group-13.g.vcf.gz.tbi, called/T1483.contig-group-13.g.vcf.gz.tbi, called/T178.contig-group-13.g.vcf.gz.tbi, called/T179.contig-group-13.g.vcf.gz.tbi, called/T180.contig-group-13.g.vcf.gz.tbi, called/T181.contig-group-13.g.vcf.gz.tbi, called/T185.contig-group-13.g.vcf.gz.tbi, called/T186.contig-group-13.g.vcf.gz.tbi, called/T187.contig-group-13.g.vcf.gz.tbi, called/T188.contig-group-13.g.vcf.gz.tbi, called/T189.contig-group-13.g.vcf.gz.tbi, called/T190.contig-group-13.g.vcf.gz.tbi, called/T192.contig-group-13.g.vcf.gz.tbi, called/T193.contig-group-13.g.vcf.gz.tbi, called/T194.contig-group-13.g.vcf.gz.tbi, called/T196.contig-group-13.g.vcf.gz.tbi, called/T248.contig-group-13.g.vcf.gz.tbi, called/T37.contig-group-13.g.vcf.gz.tbi, called/T72.contig-group-13.g.vcf.gz.tbi, called/T79.contig-group-13.g.vcf.gz.tbi output: called/all.contig-group-13.g.vcf.gz, called/all.contig-group-13.g.done log: logs/gatk/combine-gvcfs/contig-group-13.log jobid: 2653 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-13.bench.log reason: Input files updated by another job: called/N_9449.contig-group-13.g.vcf.gz.tbi, called/N_2003_5409.contig-group-13.g.vcf.gz.tbi, called/N_6489.contig-group-13.g.vcf.gz, called/N_79.contig-group-13.g.vcf.gz.tbi, called/N_83.contig-group-13.g.vcf.gz.tbi, called/N_9104.contig-group-13.g.vcf.gz.tbi, called/T187.contig-group-13.g.vcf.gz, called/T190.contig-group-13.g.vcf.gz.tbi, called/N_4847.contig-group-13.g.vcf.gz, called/N_1386.contig-group-13.g.vcf.gz.tbi, called/N_1870.contig-group-13.g.vcf.gz, called/N_1927.contig-group-13.g.vcf.gz.tbi, called/T72.contig-group-13.g.vcf.gz, called/N_6490.contig-group-13.g.vcf.gz.tbi, called/T1483.contig-group-13.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-13.g.vcf.gz, called/T79.contig-group-13.g.vcf.gz, called/M5672.contig-group-13.g.vcf.gz, called/N_1156.contig-group-13.g.vcf.gz.tbi, called/T180.contig-group-13.g.vcf.gz.tbi, called/N_8171.contig-group-13.g.vcf.gz, called/N_1157.contig-group-13.g.vcf.gz, called/N_8565.contig-group-13.g.vcf.gz, called/N_2003_5409.contig-group-13.g.vcf.gz, called/T190.contig-group-13.g.vcf.gz, called/T196.contig-group-13.g.vcf.gz.tbi, called/T192.contig-group-13.g.vcf.gz.tbi, called/N_1354.contig-group-13.g.vcf.gz, called/N_8171.contig-group-13.g.vcf.gz.tbi, called/T185.contig-group-13.g.vcf.gz.tbi, called/N_83.contig-group-13.g.vcf.gz, called/N_5129.contig-group-13.g.vcf.gz, called/T192.contig-group-13.g.vcf.gz, called/N_690.contig-group-13.g.vcf.gz.tbi, called/T196.contig-group-13.g.vcf.gz, called/N_351.contig-group-13.g.vcf.gz, called/N_8583.contig-group-13.g.vcf.gz.tbi, called/T187.contig-group-13.g.vcf.gz.tbi, called/N_1609.contig-group-13.g.vcf.gz, called/N_1158.contig-group-13.g.vcf.gz, called/T79.contig-group-13.g.vcf.gz.tbi, called/N2005.contig-group-13.g.vcf.gz, called/N_1156.contig-group-13.g.vcf.gz, called/N_9104.contig-group-13.g.vcf.gz, called/N_6490.contig-group-13.g.vcf.gz, called/N_102.contig-group-13.g.vcf.gz, called/N_1870.contig-group-13.g.vcf.gz.tbi, called/N_1992_0123.contig-group-13.g.vcf.gz.tbi, called/N_102.contig-group-13.g.vcf.gz.tbi, called/N_1158.contig-group-13.g.vcf.gz.tbi, called/N_4843.contig-group-13.g.vcf.gz.tbi, called/N_6928.contig-group-13.g.vcf.gz.tbi, called/N2005.contig-group-13.g.vcf.gz.tbi, called/N_6928.contig-group-13.g.vcf.gz, called/N_1609.contig-group-13.g.vcf.gz.tbi, called/N_689.contig-group-13.g.vcf.gz.tbi, called/N_1354.contig-group-13.g.vcf.gz.tbi, called/N_351.contig-group-13.g.vcf.gz.tbi, called/N_1386.contig-group-13.g.vcf.gz, called/N_4847.contig-group-13.g.vcf.gz.tbi, called/N_5129.contig-group-13.g.vcf.gz.tbi, called/N_9449.contig-group-13.g.vcf.gz, called/T72.contig-group-13.g.vcf.gz.tbi, called/N_79.contig-group-13.g.vcf.gz, called/T1483.contig-group-13.g.vcf.gz, called/T185.contig-group-13.g.vcf.gz, called/M5672.contig-group-13.g.vcf.gz.tbi, called/N_8565.contig-group-13.g.vcf.gz.tbi, called/N_1927.contig-group-13.g.vcf.gz, called/N_1157.contig-group-13.g.vcf.gz.tbi, called/N_1992_0123.contig-group-13.g.vcf.gz, called/N_1934_1_1_5973.contig-group-13.g.vcf.gz.tbi, called/N_8583.contig-group-13.g.vcf.gz, called/N_6489.contig-group-13.g.vcf.gz.tbi, called/T180.contig-group-13.g.vcf.gz, called/N_689.contig-group-13.g.vcf.gz, called/N_690.contig-group-13.g.vcf.gz, called/N_4843.contig-group-13.g.vcf.gz wildcards: contig=contig-group-13 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-6.g.vcf.gz, called/M1865_2.contig-group-6.g.vcf.gz, called/M5672.contig-group-6.g.vcf.gz, called/MTDC48361.contig-group-6.g.vcf.gz, called/N2005.contig-group-6.g.vcf.gz, called/N_102.contig-group-6.g.vcf.gz, called/N_1085.contig-group-6.g.vcf.gz, called/N_1156.contig-group-6.g.vcf.gz, called/N_1157.contig-group-6.g.vcf.gz, called/N_1158.contig-group-6.g.vcf.gz, called/N_1344.contig-group-6.g.vcf.gz, called/N_1347.contig-group-6.g.vcf.gz, called/N_1354.contig-group-6.g.vcf.gz, called/N_1355.contig-group-6.g.vcf.gz, called/N_1384.contig-group-6.g.vcf.gz, called/N_1386.contig-group-6.g.vcf.gz, called/N_1390.contig-group-6.g.vcf.gz, called/N_1409.contig-group-6.g.vcf.gz, called/N_1411.contig-group-6.g.vcf.gz, called/N_1413.contig-group-6.g.vcf.gz, called/N_1414.contig-group-6.g.vcf.gz, called/N_1609.contig-group-6.g.vcf.gz, called/N_1870.contig-group-6.g.vcf.gz, called/N_1901.contig-group-6.g.vcf.gz, called/N_1913.contig-group-6.g.vcf.gz, called/N_1927.contig-group-6.g.vcf.gz, called/N_192.contig-group-6.g.vcf.gz, called/N_1934_1_1_368.contig-group-6.g.vcf.gz, called/N_1934_1_1_5973.contig-group-6.g.vcf.gz, called/N_1951_13_1951.contig-group-6.g.vcf.gz, called/N_1992_0123.contig-group-6.g.vcf.gz, called/N_1998_0130.contig-group-6.g.vcf.gz, called/N_2001_0025.contig-group-6.g.vcf.gz, called/N_2001_0205.contig-group-6.g.vcf.gz, called/N_2002_0292.contig-group-6.g.vcf.gz, called/N_2003_5409.contig-group-6.g.vcf.gz, called/N_2004.contig-group-6.g.vcf.gz, called/N_2010_1759.contig-group-6.g.vcf.gz, called/N_21.contig-group-6.g.vcf.gz, called/N_351.contig-group-6.g.vcf.gz, called/N_355.contig-group-6.g.vcf.gz, called/N_401.contig-group-6.g.vcf.gz, called/N_403.contig-group-6.g.vcf.gz, called/N_4843.contig-group-6.g.vcf.gz, called/N_4844.contig-group-6.g.vcf.gz, called/N_4846.contig-group-6.g.vcf.gz, called/N_4847.contig-group-6.g.vcf.gz, called/N_5056.contig-group-6.g.vcf.gz, called/N_5057.contig-group-6.g.vcf.gz, called/N_5129.contig-group-6.g.vcf.gz, called/N_6489.contig-group-6.g.vcf.gz, called/N_6490.contig-group-6.g.vcf.gz, called/N_685.contig-group-6.g.vcf.gz, called/N_689.contig-group-6.g.vcf.gz, called/N_690.contig-group-6.g.vcf.gz, called/N_6926.contig-group-6.g.vcf.gz, called/N_6928.contig-group-6.g.vcf.gz, called/N_6932.contig-group-6.g.vcf.gz, called/N_6.contig-group-6.g.vcf.gz, called/N_7083.contig-group-6.g.vcf.gz, called/N_79.contig-group-6.g.vcf.gz, called/N_7.contig-group-6.g.vcf.gz, called/N_8105.contig-group-6.g.vcf.gz, called/N_8171.contig-group-6.g.vcf.gz, called/N_83.contig-group-6.g.vcf.gz, called/N_8564.contig-group-6.g.vcf.gz, called/N_8565.contig-group-6.g.vcf.gz, called/N_8583.contig-group-6.g.vcf.gz, called/N_8585.contig-group-6.g.vcf.gz, called/N_8586.contig-group-6.g.vcf.gz, called/N_9104.contig-group-6.g.vcf.gz, called/N_9449.contig-group-6.g.vcf.gz, called/N_94.contig-group-6.g.vcf.gz, called/T1481.contig-group-6.g.vcf.gz, called/T1483.contig-group-6.g.vcf.gz, called/T178.contig-group-6.g.vcf.gz, called/T179.contig-group-6.g.vcf.gz, called/T180.contig-group-6.g.vcf.gz, called/T181.contig-group-6.g.vcf.gz, called/T185.contig-group-6.g.vcf.gz, called/T186.contig-group-6.g.vcf.gz, called/T187.contig-group-6.g.vcf.gz, called/T188.contig-group-6.g.vcf.gz, called/T189.contig-group-6.g.vcf.gz, called/T190.contig-group-6.g.vcf.gz, called/T192.contig-group-6.g.vcf.gz, called/T193.contig-group-6.g.vcf.gz, called/T194.contig-group-6.g.vcf.gz, called/T196.contig-group-6.g.vcf.gz, called/T248.contig-group-6.g.vcf.gz, called/T37.contig-group-6.g.vcf.gz, called/T72.contig-group-6.g.vcf.gz, called/T79.contig-group-6.g.vcf.gz, called/M1864_2.contig-group-6.g.vcf.gz.tbi, called/M1865_2.contig-group-6.g.vcf.gz.tbi, called/M5672.contig-group-6.g.vcf.gz.tbi, called/MTDC48361.contig-group-6.g.vcf.gz.tbi, called/N2005.contig-group-6.g.vcf.gz.tbi, called/N_102.contig-group-6.g.vcf.gz.tbi, called/N_1085.contig-group-6.g.vcf.gz.tbi, called/N_1156.contig-group-6.g.vcf.gz.tbi, called/N_1157.contig-group-6.g.vcf.gz.tbi, called/N_1158.contig-group-6.g.vcf.gz.tbi, called/N_1344.contig-group-6.g.vcf.gz.tbi, called/N_1347.contig-group-6.g.vcf.gz.tbi, called/N_1354.contig-group-6.g.vcf.gz.tbi, called/N_1355.contig-group-6.g.vcf.gz.tbi, called/N_1384.contig-group-6.g.vcf.gz.tbi, called/N_1386.contig-group-6.g.vcf.gz.tbi, called/N_1390.contig-group-6.g.vcf.gz.tbi, called/N_1409.contig-group-6.g.vcf.gz.tbi, called/N_1411.contig-group-6.g.vcf.gz.tbi, called/N_1413.contig-group-6.g.vcf.gz.tbi, called/N_1414.contig-group-6.g.vcf.gz.tbi, called/N_1609.contig-group-6.g.vcf.gz.tbi, called/N_1870.contig-group-6.g.vcf.gz.tbi, called/N_1901.contig-group-6.g.vcf.gz.tbi, called/N_1913.contig-group-6.g.vcf.gz.tbi, called/N_1927.contig-group-6.g.vcf.gz.tbi, called/N_192.contig-group-6.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-6.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-6.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-6.g.vcf.gz.tbi, called/N_1992_0123.contig-group-6.g.vcf.gz.tbi, called/N_1998_0130.contig-group-6.g.vcf.gz.tbi, called/N_2001_0025.contig-group-6.g.vcf.gz.tbi, called/N_2001_0205.contig-group-6.g.vcf.gz.tbi, called/N_2002_0292.contig-group-6.g.vcf.gz.tbi, called/N_2003_5409.contig-group-6.g.vcf.gz.tbi, called/N_2004.contig-group-6.g.vcf.gz.tbi, called/N_2010_1759.contig-group-6.g.vcf.gz.tbi, called/N_21.contig-group-6.g.vcf.gz.tbi, called/N_351.contig-group-6.g.vcf.gz.tbi, called/N_355.contig-group-6.g.vcf.gz.tbi, called/N_401.contig-group-6.g.vcf.gz.tbi, called/N_403.contig-group-6.g.vcf.gz.tbi, called/N_4843.contig-group-6.g.vcf.gz.tbi, called/N_4844.contig-group-6.g.vcf.gz.tbi, called/N_4846.contig-group-6.g.vcf.gz.tbi, called/N_4847.contig-group-6.g.vcf.gz.tbi, called/N_5056.contig-group-6.g.vcf.gz.tbi, called/N_5057.contig-group-6.g.vcf.gz.tbi, called/N_5129.contig-group-6.g.vcf.gz.tbi, called/N_6489.contig-group-6.g.vcf.gz.tbi, called/N_6490.contig-group-6.g.vcf.gz.tbi, called/N_685.contig-group-6.g.vcf.gz.tbi, called/N_689.contig-group-6.g.vcf.gz.tbi, called/N_690.contig-group-6.g.vcf.gz.tbi, called/N_6926.contig-group-6.g.vcf.gz.tbi, called/N_6928.contig-group-6.g.vcf.gz.tbi, called/N_6932.contig-group-6.g.vcf.gz.tbi, called/N_6.contig-group-6.g.vcf.gz.tbi, called/N_7083.contig-group-6.g.vcf.gz.tbi, called/N_79.contig-group-6.g.vcf.gz.tbi, called/N_7.contig-group-6.g.vcf.gz.tbi, called/N_8105.contig-group-6.g.vcf.gz.tbi, called/N_8171.contig-group-6.g.vcf.gz.tbi, called/N_83.contig-group-6.g.vcf.gz.tbi, called/N_8564.contig-group-6.g.vcf.gz.tbi, called/N_8565.contig-group-6.g.vcf.gz.tbi, called/N_8583.contig-group-6.g.vcf.gz.tbi, called/N_8585.contig-group-6.g.vcf.gz.tbi, called/N_8586.contig-group-6.g.vcf.gz.tbi, called/N_9104.contig-group-6.g.vcf.gz.tbi, called/N_9449.contig-group-6.g.vcf.gz.tbi, called/N_94.contig-group-6.g.vcf.gz.tbi, called/T1481.contig-group-6.g.vcf.gz.tbi, called/T1483.contig-group-6.g.vcf.gz.tbi, called/T178.contig-group-6.g.vcf.gz.tbi, called/T179.contig-group-6.g.vcf.gz.tbi, called/T180.contig-group-6.g.vcf.gz.tbi, called/T181.contig-group-6.g.vcf.gz.tbi, called/T185.contig-group-6.g.vcf.gz.tbi, called/T186.contig-group-6.g.vcf.gz.tbi, called/T187.contig-group-6.g.vcf.gz.tbi, called/T188.contig-group-6.g.vcf.gz.tbi, called/T189.contig-group-6.g.vcf.gz.tbi, called/T190.contig-group-6.g.vcf.gz.tbi, called/T192.contig-group-6.g.vcf.gz.tbi, called/T193.contig-group-6.g.vcf.gz.tbi, called/T194.contig-group-6.g.vcf.gz.tbi, called/T196.contig-group-6.g.vcf.gz.tbi, called/T248.contig-group-6.g.vcf.gz.tbi, called/T37.contig-group-6.g.vcf.gz.tbi, called/T72.contig-group-6.g.vcf.gz.tbi, called/T79.contig-group-6.g.vcf.gz.tbi output: called/all.contig-group-6.g.vcf.gz, called/all.contig-group-6.g.done log: logs/gatk/combine-gvcfs/contig-group-6.log jobid: 1981 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-6.bench.log reason: Input files updated by another job: called/N_2003_5409.contig-group-6.g.vcf.gz.tbi, called/T72.contig-group-6.g.vcf.gz, called/N_351.contig-group-6.g.vcf.gz, called/N_1354.contig-group-6.g.vcf.gz.tbi, called/T187.contig-group-6.g.vcf.gz.tbi, called/N2005.contig-group-6.g.vcf.gz, called/N_6490.contig-group-6.g.vcf.gz.tbi, called/N_8565.contig-group-6.g.vcf.gz, called/T192.contig-group-6.g.vcf.gz.tbi, called/N_4843.contig-group-6.g.vcf.gz.tbi, called/N_690.contig-group-6.g.vcf.gz, called/T190.contig-group-6.g.vcf.gz, called/T185.contig-group-6.g.vcf.gz.tbi, called/N_6489.contig-group-6.g.vcf.gz.tbi, called/N_351.contig-group-6.g.vcf.gz.tbi, called/N_1157.contig-group-6.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-6.g.vcf.gz, called/T79.contig-group-6.g.vcf.gz, called/N_6490.contig-group-6.g.vcf.gz, called/T180.contig-group-6.g.vcf.gz, called/N_9449.contig-group-6.g.vcf.gz, called/N_1157.contig-group-6.g.vcf.gz, called/N_8171.contig-group-6.g.vcf.gz, called/N2005.contig-group-6.g.vcf.gz.tbi, called/N_1156.contig-group-6.g.vcf.gz, called/N_6489.contig-group-6.g.vcf.gz, called/N_1992_0123.contig-group-6.g.vcf.gz, called/N_83.contig-group-6.g.vcf.gz, called/N_1386.contig-group-6.g.vcf.gz.tbi, called/N_8171.contig-group-6.g.vcf.gz.tbi, called/N_1870.contig-group-6.g.vcf.gz.tbi, called/N_689.contig-group-6.g.vcf.gz.tbi, called/N_4847.contig-group-6.g.vcf.gz, called/N_102.contig-group-6.g.vcf.gz, called/N_690.contig-group-6.g.vcf.gz.tbi, called/N_1870.contig-group-6.g.vcf.gz, called/T190.contig-group-6.g.vcf.gz.tbi, called/N_689.contig-group-6.g.vcf.gz, called/T180.contig-group-6.g.vcf.gz.tbi, called/T187.contig-group-6.g.vcf.gz, called/N_1158.contig-group-6.g.vcf.gz, called/T192.contig-group-6.g.vcf.gz, called/T185.contig-group-6.g.vcf.gz, called/N_8583.contig-group-6.g.vcf.gz, called/M5672.contig-group-6.g.vcf.gz.tbi, called/N_1609.contig-group-6.g.vcf.gz, called/N_5129.contig-group-6.g.vcf.gz, called/N_79.contig-group-6.g.vcf.gz, called/N_8583.contig-group-6.g.vcf.gz.tbi, called/T79.contig-group-6.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-6.g.vcf.gz.tbi, called/N_4843.contig-group-6.g.vcf.gz, called/N_5129.contig-group-6.g.vcf.gz.tbi, called/N_1156.contig-group-6.g.vcf.gz.tbi, called/T196.contig-group-6.g.vcf.gz.tbi, called/N_9104.contig-group-6.g.vcf.gz, called/T72.contig-group-6.g.vcf.gz.tbi, called/N_1609.contig-group-6.g.vcf.gz.tbi, called/N_1354.contig-group-6.g.vcf.gz, called/N_6928.contig-group-6.g.vcf.gz.tbi, called/N_102.contig-group-6.g.vcf.gz.tbi, called/N_9104.contig-group-6.g.vcf.gz.tbi, called/N_1158.contig-group-6.g.vcf.gz.tbi, called/N_6928.contig-group-6.g.vcf.gz, called/T1483.contig-group-6.g.vcf.gz.tbi, called/N_8565.contig-group-6.g.vcf.gz.tbi, called/M5672.contig-group-6.g.vcf.gz, called/N_1927.contig-group-6.g.vcf.gz, called/N_83.contig-group-6.g.vcf.gz.tbi, called/T1483.contig-group-6.g.vcf.gz, called/N_1927.contig-group-6.g.vcf.gz.tbi, called/N_4847.contig-group-6.g.vcf.gz.tbi, called/N_1992_0123.contig-group-6.g.vcf.gz.tbi, called/N_79.contig-group-6.g.vcf.gz.tbi, called/N_9449.contig-group-6.g.vcf.gz.tbi, called/T196.contig-group-6.g.vcf.gz, called/N_2003_5409.contig-group-6.g.vcf.gz, called/N_1386.contig-group-6.g.vcf.gz wildcards: contig=contig-group-6 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-4.g.vcf.gz, called/M1865_2.contig-group-4.g.vcf.gz, called/M5672.contig-group-4.g.vcf.gz, called/MTDC48361.contig-group-4.g.vcf.gz, called/N2005.contig-group-4.g.vcf.gz, called/N_102.contig-group-4.g.vcf.gz, called/N_1085.contig-group-4.g.vcf.gz, called/N_1156.contig-group-4.g.vcf.gz, called/N_1157.contig-group-4.g.vcf.gz, called/N_1158.contig-group-4.g.vcf.gz, called/N_1344.contig-group-4.g.vcf.gz, called/N_1347.contig-group-4.g.vcf.gz, called/N_1354.contig-group-4.g.vcf.gz, called/N_1355.contig-group-4.g.vcf.gz, called/N_1384.contig-group-4.g.vcf.gz, called/N_1386.contig-group-4.g.vcf.gz, called/N_1390.contig-group-4.g.vcf.gz, called/N_1409.contig-group-4.g.vcf.gz, called/N_1411.contig-group-4.g.vcf.gz, called/N_1413.contig-group-4.g.vcf.gz, called/N_1414.contig-group-4.g.vcf.gz, called/N_1609.contig-group-4.g.vcf.gz, called/N_1870.contig-group-4.g.vcf.gz, called/N_1901.contig-group-4.g.vcf.gz, called/N_1913.contig-group-4.g.vcf.gz, called/N_1927.contig-group-4.g.vcf.gz, called/N_192.contig-group-4.g.vcf.gz, called/N_1934_1_1_368.contig-group-4.g.vcf.gz, called/N_1934_1_1_5973.contig-group-4.g.vcf.gz, called/N_1951_13_1951.contig-group-4.g.vcf.gz, called/N_1992_0123.contig-group-4.g.vcf.gz, called/N_1998_0130.contig-group-4.g.vcf.gz, called/N_2001_0025.contig-group-4.g.vcf.gz, called/N_2001_0205.contig-group-4.g.vcf.gz, called/N_2002_0292.contig-group-4.g.vcf.gz, called/N_2003_5409.contig-group-4.g.vcf.gz, called/N_2004.contig-group-4.g.vcf.gz, called/N_2010_1759.contig-group-4.g.vcf.gz, called/N_21.contig-group-4.g.vcf.gz, called/N_351.contig-group-4.g.vcf.gz, called/N_355.contig-group-4.g.vcf.gz, called/N_401.contig-group-4.g.vcf.gz, called/N_403.contig-group-4.g.vcf.gz, called/N_4843.contig-group-4.g.vcf.gz, called/N_4844.contig-group-4.g.vcf.gz, called/N_4846.contig-group-4.g.vcf.gz, called/N_4847.contig-group-4.g.vcf.gz, called/N_5056.contig-group-4.g.vcf.gz, called/N_5057.contig-group-4.g.vcf.gz, called/N_5129.contig-group-4.g.vcf.gz, called/N_6489.contig-group-4.g.vcf.gz, called/N_6490.contig-group-4.g.vcf.gz, called/N_685.contig-group-4.g.vcf.gz, called/N_689.contig-group-4.g.vcf.gz, called/N_690.contig-group-4.g.vcf.gz, called/N_6926.contig-group-4.g.vcf.gz, called/N_6928.contig-group-4.g.vcf.gz, called/N_6932.contig-group-4.g.vcf.gz, called/N_6.contig-group-4.g.vcf.gz, called/N_7083.contig-group-4.g.vcf.gz, called/N_79.contig-group-4.g.vcf.gz, called/N_7.contig-group-4.g.vcf.gz, called/N_8105.contig-group-4.g.vcf.gz, called/N_8171.contig-group-4.g.vcf.gz, called/N_83.contig-group-4.g.vcf.gz, called/N_8564.contig-group-4.g.vcf.gz, called/N_8565.contig-group-4.g.vcf.gz, called/N_8583.contig-group-4.g.vcf.gz, called/N_8585.contig-group-4.g.vcf.gz, called/N_8586.contig-group-4.g.vcf.gz, called/N_9104.contig-group-4.g.vcf.gz, called/N_9449.contig-group-4.g.vcf.gz, called/N_94.contig-group-4.g.vcf.gz, called/T1481.contig-group-4.g.vcf.gz, called/T1483.contig-group-4.g.vcf.gz, called/T178.contig-group-4.g.vcf.gz, called/T179.contig-group-4.g.vcf.gz, called/T180.contig-group-4.g.vcf.gz, called/T181.contig-group-4.g.vcf.gz, called/T185.contig-group-4.g.vcf.gz, called/T186.contig-group-4.g.vcf.gz, called/T187.contig-group-4.g.vcf.gz, called/T188.contig-group-4.g.vcf.gz, called/T189.contig-group-4.g.vcf.gz, called/T190.contig-group-4.g.vcf.gz, called/T192.contig-group-4.g.vcf.gz, called/T193.contig-group-4.g.vcf.gz, called/T194.contig-group-4.g.vcf.gz, called/T196.contig-group-4.g.vcf.gz, called/T248.contig-group-4.g.vcf.gz, called/T37.contig-group-4.g.vcf.gz, called/T72.contig-group-4.g.vcf.gz, called/T79.contig-group-4.g.vcf.gz, called/M1864_2.contig-group-4.g.vcf.gz.tbi, called/M1865_2.contig-group-4.g.vcf.gz.tbi, called/M5672.contig-group-4.g.vcf.gz.tbi, called/MTDC48361.contig-group-4.g.vcf.gz.tbi, called/N2005.contig-group-4.g.vcf.gz.tbi, called/N_102.contig-group-4.g.vcf.gz.tbi, called/N_1085.contig-group-4.g.vcf.gz.tbi, called/N_1156.contig-group-4.g.vcf.gz.tbi, called/N_1157.contig-group-4.g.vcf.gz.tbi, called/N_1158.contig-group-4.g.vcf.gz.tbi, called/N_1344.contig-group-4.g.vcf.gz.tbi, called/N_1347.contig-group-4.g.vcf.gz.tbi, called/N_1354.contig-group-4.g.vcf.gz.tbi, called/N_1355.contig-group-4.g.vcf.gz.tbi, called/N_1384.contig-group-4.g.vcf.gz.tbi, called/N_1386.contig-group-4.g.vcf.gz.tbi, called/N_1390.contig-group-4.g.vcf.gz.tbi, called/N_1409.contig-group-4.g.vcf.gz.tbi, called/N_1411.contig-group-4.g.vcf.gz.tbi, called/N_1413.contig-group-4.g.vcf.gz.tbi, called/N_1414.contig-group-4.g.vcf.gz.tbi, called/N_1609.contig-group-4.g.vcf.gz.tbi, called/N_1870.contig-group-4.g.vcf.gz.tbi, called/N_1901.contig-group-4.g.vcf.gz.tbi, called/N_1913.contig-group-4.g.vcf.gz.tbi, called/N_1927.contig-group-4.g.vcf.gz.tbi, called/N_192.contig-group-4.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-4.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-4.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-4.g.vcf.gz.tbi, called/N_1992_0123.contig-group-4.g.vcf.gz.tbi, called/N_1998_0130.contig-group-4.g.vcf.gz.tbi, called/N_2001_0025.contig-group-4.g.vcf.gz.tbi, called/N_2001_0205.contig-group-4.g.vcf.gz.tbi, called/N_2002_0292.contig-group-4.g.vcf.gz.tbi, called/N_2003_5409.contig-group-4.g.vcf.gz.tbi, called/N_2004.contig-group-4.g.vcf.gz.tbi, called/N_2010_1759.contig-group-4.g.vcf.gz.tbi, called/N_21.contig-group-4.g.vcf.gz.tbi, called/N_351.contig-group-4.g.vcf.gz.tbi, called/N_355.contig-group-4.g.vcf.gz.tbi, called/N_401.contig-group-4.g.vcf.gz.tbi, called/N_403.contig-group-4.g.vcf.gz.tbi, called/N_4843.contig-group-4.g.vcf.gz.tbi, called/N_4844.contig-group-4.g.vcf.gz.tbi, called/N_4846.contig-group-4.g.vcf.gz.tbi, called/N_4847.contig-group-4.g.vcf.gz.tbi, called/N_5056.contig-group-4.g.vcf.gz.tbi, called/N_5057.contig-group-4.g.vcf.gz.tbi, called/N_5129.contig-group-4.g.vcf.gz.tbi, called/N_6489.contig-group-4.g.vcf.gz.tbi, called/N_6490.contig-group-4.g.vcf.gz.tbi, called/N_685.contig-group-4.g.vcf.gz.tbi, called/N_689.contig-group-4.g.vcf.gz.tbi, called/N_690.contig-group-4.g.vcf.gz.tbi, called/N_6926.contig-group-4.g.vcf.gz.tbi, called/N_6928.contig-group-4.g.vcf.gz.tbi, called/N_6932.contig-group-4.g.vcf.gz.tbi, called/N_6.contig-group-4.g.vcf.gz.tbi, called/N_7083.contig-group-4.g.vcf.gz.tbi, called/N_79.contig-group-4.g.vcf.gz.tbi, called/N_7.contig-group-4.g.vcf.gz.tbi, called/N_8105.contig-group-4.g.vcf.gz.tbi, called/N_8171.contig-group-4.g.vcf.gz.tbi, called/N_83.contig-group-4.g.vcf.gz.tbi, called/N_8564.contig-group-4.g.vcf.gz.tbi, called/N_8565.contig-group-4.g.vcf.gz.tbi, called/N_8583.contig-group-4.g.vcf.gz.tbi, called/N_8585.contig-group-4.g.vcf.gz.tbi, called/N_8586.contig-group-4.g.vcf.gz.tbi, called/N_9104.contig-group-4.g.vcf.gz.tbi, called/N_9449.contig-group-4.g.vcf.gz.tbi, called/N_94.contig-group-4.g.vcf.gz.tbi, called/T1481.contig-group-4.g.vcf.gz.tbi, called/T1483.contig-group-4.g.vcf.gz.tbi, called/T178.contig-group-4.g.vcf.gz.tbi, called/T179.contig-group-4.g.vcf.gz.tbi, called/T180.contig-group-4.g.vcf.gz.tbi, called/T181.contig-group-4.g.vcf.gz.tbi, called/T185.contig-group-4.g.vcf.gz.tbi, called/T186.contig-group-4.g.vcf.gz.tbi, called/T187.contig-group-4.g.vcf.gz.tbi, called/T188.contig-group-4.g.vcf.gz.tbi, called/T189.contig-group-4.g.vcf.gz.tbi, called/T190.contig-group-4.g.vcf.gz.tbi, called/T192.contig-group-4.g.vcf.gz.tbi, called/T193.contig-group-4.g.vcf.gz.tbi, called/T194.contig-group-4.g.vcf.gz.tbi, called/T196.contig-group-4.g.vcf.gz.tbi, called/T248.contig-group-4.g.vcf.gz.tbi, called/T37.contig-group-4.g.vcf.gz.tbi, called/T72.contig-group-4.g.vcf.gz.tbi, called/T79.contig-group-4.g.vcf.gz.tbi output: called/all.contig-group-4.g.vcf.gz, called/all.contig-group-4.g.done log: logs/gatk/combine-gvcfs/contig-group-4.log jobid: 1789 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-4.bench.log reason: Input files updated by another job: called/N_1354.contig-group-4.g.vcf.gz, called/T192.contig-group-4.g.vcf.gz, called/N_9449.contig-group-4.g.vcf.gz, called/N_1609.contig-group-4.g.vcf.gz, called/N_5129.contig-group-4.g.vcf.gz.tbi, called/N2005.contig-group-4.g.vcf.gz.tbi, called/N_1158.contig-group-4.g.vcf.gz, called/N_1934_1_1_5973.contig-group-4.g.vcf.gz, called/T72.contig-group-4.g.vcf.gz, called/T1483.contig-group-4.g.vcf.gz.tbi, called/T79.contig-group-4.g.vcf.gz, called/N_351.contig-group-4.g.vcf.gz, called/N_2003_5409.contig-group-4.g.vcf.gz.tbi, called/N_1157.contig-group-4.g.vcf.gz.tbi, called/N_8583.contig-group-4.g.vcf.gz, called/T187.contig-group-4.g.vcf.gz, called/N_83.contig-group-4.g.vcf.gz, called/N_1157.contig-group-4.g.vcf.gz, called/N_6490.contig-group-4.g.vcf.gz.tbi, called/T196.contig-group-4.g.vcf.gz.tbi, called/N_690.contig-group-4.g.vcf.gz, called/T185.contig-group-4.g.vcf.gz, called/T180.contig-group-4.g.vcf.gz.tbi, called/N_79.contig-group-4.g.vcf.gz, called/N2005.contig-group-4.g.vcf.gz, called/N_6490.contig-group-4.g.vcf.gz, called/N_6928.contig-group-4.g.vcf.gz.tbi, called/M5672.contig-group-4.g.vcf.gz, called/T187.contig-group-4.g.vcf.gz.tbi, called/T196.contig-group-4.g.vcf.gz, called/N_1992_0123.contig-group-4.g.vcf.gz.tbi, called/T79.contig-group-4.g.vcf.gz.tbi, called/N_1156.contig-group-4.g.vcf.gz.tbi, called/N_8565.contig-group-4.g.vcf.gz.tbi, called/T185.contig-group-4.g.vcf.gz.tbi, called/N_1354.contig-group-4.g.vcf.gz.tbi, called/T180.contig-group-4.g.vcf.gz, called/N_4847.contig-group-4.g.vcf.gz, called/T190.contig-group-4.g.vcf.gz, called/N_8565.contig-group-4.g.vcf.gz, called/N_1870.contig-group-4.g.vcf.gz, called/N_689.contig-group-4.g.vcf.gz, called/N_83.contig-group-4.g.vcf.gz.tbi, called/N_8171.contig-group-4.g.vcf.gz.tbi, called/N_9104.contig-group-4.g.vcf.gz.tbi, called/T72.contig-group-4.g.vcf.gz.tbi, called/N_1609.contig-group-4.g.vcf.gz.tbi, called/N_1158.contig-group-4.g.vcf.gz.tbi, called/N_2003_5409.contig-group-4.g.vcf.gz, called/N_1934_1_1_5973.contig-group-4.g.vcf.gz.tbi, called/N_9104.contig-group-4.g.vcf.gz, called/N_1927.contig-group-4.g.vcf.gz, called/M5672.contig-group-4.g.vcf.gz.tbi, called/N_4843.contig-group-4.g.vcf.gz.tbi, called/N_9449.contig-group-4.g.vcf.gz.tbi, called/N_351.contig-group-4.g.vcf.gz.tbi, called/N_6489.contig-group-4.g.vcf.gz.tbi, called/N_8171.contig-group-4.g.vcf.gz, called/N_1927.contig-group-4.g.vcf.gz.tbi, called/N_6928.contig-group-4.g.vcf.gz, called/N_102.contig-group-4.g.vcf.gz, called/N_5129.contig-group-4.g.vcf.gz, called/N_4847.contig-group-4.g.vcf.gz.tbi, called/N_1156.contig-group-4.g.vcf.gz, called/T192.contig-group-4.g.vcf.gz.tbi, called/N_1386.contig-group-4.g.vcf.gz, called/N_8583.contig-group-4.g.vcf.gz.tbi, called/N_4843.contig-group-4.g.vcf.gz, called/N_79.contig-group-4.g.vcf.gz.tbi, called/N_689.contig-group-4.g.vcf.gz.tbi, called/N_102.contig-group-4.g.vcf.gz.tbi, called/N_690.contig-group-4.g.vcf.gz.tbi, called/T190.contig-group-4.g.vcf.gz.tbi, called/N_1870.contig-group-4.g.vcf.gz.tbi, called/N_6489.contig-group-4.g.vcf.gz, called/T1483.contig-group-4.g.vcf.gz, called/N_1386.contig-group-4.g.vcf.gz.tbi, called/N_1992_0123.contig-group-4.g.vcf.gz wildcards: contig=contig-group-4 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-25.g.vcf.gz, called/M1865_2.contig-group-25.g.vcf.gz, called/M5672.contig-group-25.g.vcf.gz, called/MTDC48361.contig-group-25.g.vcf.gz, called/N2005.contig-group-25.g.vcf.gz, called/N_102.contig-group-25.g.vcf.gz, called/N_1085.contig-group-25.g.vcf.gz, called/N_1156.contig-group-25.g.vcf.gz, called/N_1157.contig-group-25.g.vcf.gz, called/N_1158.contig-group-25.g.vcf.gz, called/N_1344.contig-group-25.g.vcf.gz, called/N_1347.contig-group-25.g.vcf.gz, called/N_1354.contig-group-25.g.vcf.gz, called/N_1355.contig-group-25.g.vcf.gz, called/N_1384.contig-group-25.g.vcf.gz, called/N_1386.contig-group-25.g.vcf.gz, called/N_1390.contig-group-25.g.vcf.gz, called/N_1409.contig-group-25.g.vcf.gz, called/N_1411.contig-group-25.g.vcf.gz, called/N_1413.contig-group-25.g.vcf.gz, called/N_1414.contig-group-25.g.vcf.gz, called/N_1609.contig-group-25.g.vcf.gz, called/N_1870.contig-group-25.g.vcf.gz, called/N_1901.contig-group-25.g.vcf.gz, called/N_1913.contig-group-25.g.vcf.gz, called/N_1927.contig-group-25.g.vcf.gz, called/N_192.contig-group-25.g.vcf.gz, called/N_1934_1_1_368.contig-group-25.g.vcf.gz, called/N_1934_1_1_5973.contig-group-25.g.vcf.gz, called/N_1951_13_1951.contig-group-25.g.vcf.gz, called/N_1992_0123.contig-group-25.g.vcf.gz, called/N_1998_0130.contig-group-25.g.vcf.gz, called/N_2001_0025.contig-group-25.g.vcf.gz, called/N_2001_0205.contig-group-25.g.vcf.gz, called/N_2002_0292.contig-group-25.g.vcf.gz, called/N_2003_5409.contig-group-25.g.vcf.gz, called/N_2004.contig-group-25.g.vcf.gz, called/N_2010_1759.contig-group-25.g.vcf.gz, called/N_21.contig-group-25.g.vcf.gz, called/N_351.contig-group-25.g.vcf.gz, called/N_355.contig-group-25.g.vcf.gz, called/N_401.contig-group-25.g.vcf.gz, called/N_403.contig-group-25.g.vcf.gz, called/N_4843.contig-group-25.g.vcf.gz, called/N_4844.contig-group-25.g.vcf.gz, called/N_4846.contig-group-25.g.vcf.gz, called/N_4847.contig-group-25.g.vcf.gz, called/N_5056.contig-group-25.g.vcf.gz, called/N_5057.contig-group-25.g.vcf.gz, called/N_5129.contig-group-25.g.vcf.gz, called/N_6489.contig-group-25.g.vcf.gz, called/N_6490.contig-group-25.g.vcf.gz, called/N_685.contig-group-25.g.vcf.gz, called/N_689.contig-group-25.g.vcf.gz, called/N_690.contig-group-25.g.vcf.gz, called/N_6926.contig-group-25.g.vcf.gz, called/N_6928.contig-group-25.g.vcf.gz, called/N_6932.contig-group-25.g.vcf.gz, called/N_6.contig-group-25.g.vcf.gz, called/N_7083.contig-group-25.g.vcf.gz, called/N_79.contig-group-25.g.vcf.gz, called/N_7.contig-group-25.g.vcf.gz, called/N_8105.contig-group-25.g.vcf.gz, called/N_8171.contig-group-25.g.vcf.gz, called/N_83.contig-group-25.g.vcf.gz, called/N_8564.contig-group-25.g.vcf.gz, called/N_8565.contig-group-25.g.vcf.gz, called/N_8583.contig-group-25.g.vcf.gz, called/N_8585.contig-group-25.g.vcf.gz, called/N_8586.contig-group-25.g.vcf.gz, called/N_9104.contig-group-25.g.vcf.gz, called/N_9449.contig-group-25.g.vcf.gz, called/N_94.contig-group-25.g.vcf.gz, called/T1481.contig-group-25.g.vcf.gz, called/T1483.contig-group-25.g.vcf.gz, called/T178.contig-group-25.g.vcf.gz, called/T179.contig-group-25.g.vcf.gz, called/T180.contig-group-25.g.vcf.gz, called/T181.contig-group-25.g.vcf.gz, called/T185.contig-group-25.g.vcf.gz, called/T186.contig-group-25.g.vcf.gz, called/T187.contig-group-25.g.vcf.gz, called/T188.contig-group-25.g.vcf.gz, called/T189.contig-group-25.g.vcf.gz, called/T190.contig-group-25.g.vcf.gz, called/T192.contig-group-25.g.vcf.gz, called/T193.contig-group-25.g.vcf.gz, called/T194.contig-group-25.g.vcf.gz, called/T196.contig-group-25.g.vcf.gz, called/T248.contig-group-25.g.vcf.gz, called/T37.contig-group-25.g.vcf.gz, called/T72.contig-group-25.g.vcf.gz, called/T79.contig-group-25.g.vcf.gz, called/M1864_2.contig-group-25.g.vcf.gz.tbi, called/M1865_2.contig-group-25.g.vcf.gz.tbi, called/M5672.contig-group-25.g.vcf.gz.tbi, called/MTDC48361.contig-group-25.g.vcf.gz.tbi, called/N2005.contig-group-25.g.vcf.gz.tbi, called/N_102.contig-group-25.g.vcf.gz.tbi, called/N_1085.contig-group-25.g.vcf.gz.tbi, called/N_1156.contig-group-25.g.vcf.gz.tbi, called/N_1157.contig-group-25.g.vcf.gz.tbi, called/N_1158.contig-group-25.g.vcf.gz.tbi, called/N_1344.contig-group-25.g.vcf.gz.tbi, called/N_1347.contig-group-25.g.vcf.gz.tbi, called/N_1354.contig-group-25.g.vcf.gz.tbi, called/N_1355.contig-group-25.g.vcf.gz.tbi, called/N_1384.contig-group-25.g.vcf.gz.tbi, called/N_1386.contig-group-25.g.vcf.gz.tbi, called/N_1390.contig-group-25.g.vcf.gz.tbi, called/N_1409.contig-group-25.g.vcf.gz.tbi, called/N_1411.contig-group-25.g.vcf.gz.tbi, called/N_1413.contig-group-25.g.vcf.gz.tbi, called/N_1414.contig-group-25.g.vcf.gz.tbi, called/N_1609.contig-group-25.g.vcf.gz.tbi, called/N_1870.contig-group-25.g.vcf.gz.tbi, called/N_1901.contig-group-25.g.vcf.gz.tbi, called/N_1913.contig-group-25.g.vcf.gz.tbi, called/N_1927.contig-group-25.g.vcf.gz.tbi, called/N_192.contig-group-25.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-25.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-25.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-25.g.vcf.gz.tbi, called/N_1992_0123.contig-group-25.g.vcf.gz.tbi, called/N_1998_0130.contig-group-25.g.vcf.gz.tbi, called/N_2001_0025.contig-group-25.g.vcf.gz.tbi, called/N_2001_0205.contig-group-25.g.vcf.gz.tbi, called/N_2002_0292.contig-group-25.g.vcf.gz.tbi, called/N_2003_5409.contig-group-25.g.vcf.gz.tbi, called/N_2004.contig-group-25.g.vcf.gz.tbi, called/N_2010_1759.contig-group-25.g.vcf.gz.tbi, called/N_21.contig-group-25.g.vcf.gz.tbi, called/N_351.contig-group-25.g.vcf.gz.tbi, called/N_355.contig-group-25.g.vcf.gz.tbi, called/N_401.contig-group-25.g.vcf.gz.tbi, called/N_403.contig-group-25.g.vcf.gz.tbi, called/N_4843.contig-group-25.g.vcf.gz.tbi, called/N_4844.contig-group-25.g.vcf.gz.tbi, called/N_4846.contig-group-25.g.vcf.gz.tbi, called/N_4847.contig-group-25.g.vcf.gz.tbi, called/N_5056.contig-group-25.g.vcf.gz.tbi, called/N_5057.contig-group-25.g.vcf.gz.tbi, called/N_5129.contig-group-25.g.vcf.gz.tbi, called/N_6489.contig-group-25.g.vcf.gz.tbi, called/N_6490.contig-group-25.g.vcf.gz.tbi, called/N_685.contig-group-25.g.vcf.gz.tbi, called/N_689.contig-group-25.g.vcf.gz.tbi, called/N_690.contig-group-25.g.vcf.gz.tbi, called/N_6926.contig-group-25.g.vcf.gz.tbi, called/N_6928.contig-group-25.g.vcf.gz.tbi, called/N_6932.contig-group-25.g.vcf.gz.tbi, called/N_6.contig-group-25.g.vcf.gz.tbi, called/N_7083.contig-group-25.g.vcf.gz.tbi, called/N_79.contig-group-25.g.vcf.gz.tbi, called/N_7.contig-group-25.g.vcf.gz.tbi, called/N_8105.contig-group-25.g.vcf.gz.tbi, called/N_8171.contig-group-25.g.vcf.gz.tbi, called/N_83.contig-group-25.g.vcf.gz.tbi, called/N_8564.contig-group-25.g.vcf.gz.tbi, called/N_8565.contig-group-25.g.vcf.gz.tbi, called/N_8583.contig-group-25.g.vcf.gz.tbi, called/N_8585.contig-group-25.g.vcf.gz.tbi, called/N_8586.contig-group-25.g.vcf.gz.tbi, called/N_9104.contig-group-25.g.vcf.gz.tbi, called/N_9449.contig-group-25.g.vcf.gz.tbi, called/N_94.contig-group-25.g.vcf.gz.tbi, called/T1481.contig-group-25.g.vcf.gz.tbi, called/T1483.contig-group-25.g.vcf.gz.tbi, called/T178.contig-group-25.g.vcf.gz.tbi, called/T179.contig-group-25.g.vcf.gz.tbi, called/T180.contig-group-25.g.vcf.gz.tbi, called/T181.contig-group-25.g.vcf.gz.tbi, called/T185.contig-group-25.g.vcf.gz.tbi, called/T186.contig-group-25.g.vcf.gz.tbi, called/T187.contig-group-25.g.vcf.gz.tbi, called/T188.contig-group-25.g.vcf.gz.tbi, called/T189.contig-group-25.g.vcf.gz.tbi, called/T190.contig-group-25.g.vcf.gz.tbi, called/T192.contig-group-25.g.vcf.gz.tbi, called/T193.contig-group-25.g.vcf.gz.tbi, called/T194.contig-group-25.g.vcf.gz.tbi, called/T196.contig-group-25.g.vcf.gz.tbi, called/T248.contig-group-25.g.vcf.gz.tbi, called/T37.contig-group-25.g.vcf.gz.tbi, called/T72.contig-group-25.g.vcf.gz.tbi, called/T79.contig-group-25.g.vcf.gz.tbi output: called/all.contig-group-25.g.vcf.gz, called/all.contig-group-25.g.done log: logs/gatk/combine-gvcfs/contig-group-25.log jobid: 3805 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-25.bench.log reason: Input files updated by another job: called/T72.contig-group-25.g.vcf.gz, called/M5672.contig-group-25.g.vcf.gz, called/N_5129.contig-group-25.g.vcf.gz, called/T180.contig-group-25.g.vcf.gz, called/N_6489.contig-group-25.g.vcf.gz, called/T187.contig-group-25.g.vcf.gz, called/N_351.contig-group-25.g.vcf.gz, called/N_1354.contig-group-25.g.vcf.gz.tbi, called/N_2003_5409.contig-group-25.g.vcf.gz, called/N_1386.contig-group-25.g.vcf.gz, called/N_1870.contig-group-25.g.vcf.gz, called/T196.contig-group-25.g.vcf.gz, called/N_2003_5409.contig-group-25.g.vcf.gz.tbi, called/N_1157.contig-group-25.g.vcf.gz.tbi, called/N_8565.contig-group-25.g.vcf.gz.tbi, called/N_8171.contig-group-25.g.vcf.gz.tbi, called/T79.contig-group-25.g.vcf.gz, called/N_4847.contig-group-25.g.vcf.gz.tbi, called/N_4843.contig-group-25.g.vcf.gz, called/N_1934_1_1_5973.contig-group-25.g.vcf.gz.tbi, called/N_4847.contig-group-25.g.vcf.gz, called/N_9449.contig-group-25.g.vcf.gz.tbi, called/T1483.contig-group-25.g.vcf.gz.tbi, called/N_6490.contig-group-25.g.vcf.gz, called/N_8565.contig-group-25.g.vcf.gz, called/N_5129.contig-group-25.g.vcf.gz.tbi, called/N_9104.contig-group-25.g.vcf.gz, called/N_1927.contig-group-25.g.vcf.gz, called/T187.contig-group-25.g.vcf.gz.tbi, called/N_689.contig-group-25.g.vcf.gz.tbi, called/N_79.contig-group-25.g.vcf.gz, called/M5672.contig-group-25.g.vcf.gz.tbi, called/N_1158.contig-group-25.g.vcf.gz.tbi, called/N_1157.contig-group-25.g.vcf.gz, called/N_79.contig-group-25.g.vcf.gz.tbi, called/N2005.contig-group-25.g.vcf.gz, called/N_1158.contig-group-25.g.vcf.gz, called/T185.contig-group-25.g.vcf.gz.tbi, called/T72.contig-group-25.g.vcf.gz.tbi, called/N_8171.contig-group-25.g.vcf.gz, called/N_102.contig-group-25.g.vcf.gz.tbi, called/N_9449.contig-group-25.g.vcf.gz, called/T79.contig-group-25.g.vcf.gz.tbi, called/N_83.contig-group-25.g.vcf.gz, called/T192.contig-group-25.g.vcf.gz, called/N_1156.contig-group-25.g.vcf.gz, called/N_102.contig-group-25.g.vcf.gz, called/N_689.contig-group-25.g.vcf.gz, called/T1483.contig-group-25.g.vcf.gz, called/N_6490.contig-group-25.g.vcf.gz.tbi, called/N_6928.contig-group-25.g.vcf.gz.tbi, called/N_9104.contig-group-25.g.vcf.gz.tbi, called/N_6928.contig-group-25.g.vcf.gz, called/N_4843.contig-group-25.g.vcf.gz.tbi, called/N_1386.contig-group-25.g.vcf.gz.tbi, called/N_690.contig-group-25.g.vcf.gz, called/N_1609.contig-group-25.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-25.g.vcf.gz, called/T185.contig-group-25.g.vcf.gz, called/N_351.contig-group-25.g.vcf.gz.tbi, called/T190.contig-group-25.g.vcf.gz.tbi, called/N_8583.contig-group-25.g.vcf.gz.tbi, called/N_8583.contig-group-25.g.vcf.gz, called/T190.contig-group-25.g.vcf.gz, called/N_1156.contig-group-25.g.vcf.gz.tbi, called/N_1609.contig-group-25.g.vcf.gz, called/T180.contig-group-25.g.vcf.gz.tbi, called/N_1354.contig-group-25.g.vcf.gz, called/N_83.contig-group-25.g.vcf.gz.tbi, called/T196.contig-group-25.g.vcf.gz.tbi, called/N_1927.contig-group-25.g.vcf.gz.tbi, called/T192.contig-group-25.g.vcf.gz.tbi, called/N_1870.contig-group-25.g.vcf.gz.tbi, called/N2005.contig-group-25.g.vcf.gz.tbi, called/N_1992_0123.contig-group-25.g.vcf.gz, called/N_690.contig-group-25.g.vcf.gz.tbi, called/N_6489.contig-group-25.g.vcf.gz.tbi, called/N_1992_0123.contig-group-25.g.vcf.gz.tbi wildcards: contig=contig-group-25 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-0.g.vcf.gz, called/M1865_2.contig-group-0.g.vcf.gz, called/M5672.contig-group-0.g.vcf.gz, called/MTDC48361.contig-group-0.g.vcf.gz, called/N2005.contig-group-0.g.vcf.gz, called/N_102.contig-group-0.g.vcf.gz, called/N_1085.contig-group-0.g.vcf.gz, called/N_1156.contig-group-0.g.vcf.gz, called/N_1157.contig-group-0.g.vcf.gz, called/N_1158.contig-group-0.g.vcf.gz, called/N_1344.contig-group-0.g.vcf.gz, called/N_1347.contig-group-0.g.vcf.gz, called/N_1354.contig-group-0.g.vcf.gz, called/N_1355.contig-group-0.g.vcf.gz, called/N_1384.contig-group-0.g.vcf.gz, called/N_1386.contig-group-0.g.vcf.gz, called/N_1390.contig-group-0.g.vcf.gz, called/N_1409.contig-group-0.g.vcf.gz, called/N_1411.contig-group-0.g.vcf.gz, called/N_1413.contig-group-0.g.vcf.gz, called/N_1414.contig-group-0.g.vcf.gz, called/N_1609.contig-group-0.g.vcf.gz, called/N_1870.contig-group-0.g.vcf.gz, called/N_1901.contig-group-0.g.vcf.gz, called/N_1913.contig-group-0.g.vcf.gz, called/N_1927.contig-group-0.g.vcf.gz, called/N_192.contig-group-0.g.vcf.gz, called/N_1934_1_1_368.contig-group-0.g.vcf.gz, called/N_1934_1_1_5973.contig-group-0.g.vcf.gz, called/N_1951_13_1951.contig-group-0.g.vcf.gz, called/N_1992_0123.contig-group-0.g.vcf.gz, called/N_1998_0130.contig-group-0.g.vcf.gz, called/N_2001_0025.contig-group-0.g.vcf.gz, called/N_2001_0205.contig-group-0.g.vcf.gz, called/N_2002_0292.contig-group-0.g.vcf.gz, called/N_2003_5409.contig-group-0.g.vcf.gz, called/N_2004.contig-group-0.g.vcf.gz, called/N_2010_1759.contig-group-0.g.vcf.gz, called/N_21.contig-group-0.g.vcf.gz, called/N_351.contig-group-0.g.vcf.gz, called/N_355.contig-group-0.g.vcf.gz, called/N_401.contig-group-0.g.vcf.gz, called/N_403.contig-group-0.g.vcf.gz, called/N_4843.contig-group-0.g.vcf.gz, called/N_4844.contig-group-0.g.vcf.gz, called/N_4846.contig-group-0.g.vcf.gz, called/N_4847.contig-group-0.g.vcf.gz, called/N_5056.contig-group-0.g.vcf.gz, called/N_5057.contig-group-0.g.vcf.gz, called/N_5129.contig-group-0.g.vcf.gz, called/N_6489.contig-group-0.g.vcf.gz, called/N_6490.contig-group-0.g.vcf.gz, called/N_685.contig-group-0.g.vcf.gz, called/N_689.contig-group-0.g.vcf.gz, called/N_690.contig-group-0.g.vcf.gz, called/N_6926.contig-group-0.g.vcf.gz, called/N_6928.contig-group-0.g.vcf.gz, called/N_6932.contig-group-0.g.vcf.gz, called/N_6.contig-group-0.g.vcf.gz, called/N_7083.contig-group-0.g.vcf.gz, called/N_79.contig-group-0.g.vcf.gz, called/N_7.contig-group-0.g.vcf.gz, called/N_8105.contig-group-0.g.vcf.gz, called/N_8171.contig-group-0.g.vcf.gz, called/N_83.contig-group-0.g.vcf.gz, called/N_8564.contig-group-0.g.vcf.gz, called/N_8565.contig-group-0.g.vcf.gz, called/N_8583.contig-group-0.g.vcf.gz, called/N_8585.contig-group-0.g.vcf.gz, called/N_8586.contig-group-0.g.vcf.gz, called/N_9104.contig-group-0.g.vcf.gz, called/N_9449.contig-group-0.g.vcf.gz, called/N_94.contig-group-0.g.vcf.gz, called/T1481.contig-group-0.g.vcf.gz, called/T1483.contig-group-0.g.vcf.gz, called/T178.contig-group-0.g.vcf.gz, called/T179.contig-group-0.g.vcf.gz, called/T180.contig-group-0.g.vcf.gz, called/T181.contig-group-0.g.vcf.gz, called/T185.contig-group-0.g.vcf.gz, called/T186.contig-group-0.g.vcf.gz, called/T187.contig-group-0.g.vcf.gz, called/T188.contig-group-0.g.vcf.gz, called/T189.contig-group-0.g.vcf.gz, called/T190.contig-group-0.g.vcf.gz, called/T192.contig-group-0.g.vcf.gz, called/T193.contig-group-0.g.vcf.gz, called/T194.contig-group-0.g.vcf.gz, called/T196.contig-group-0.g.vcf.gz, called/T248.contig-group-0.g.vcf.gz, called/T37.contig-group-0.g.vcf.gz, called/T72.contig-group-0.g.vcf.gz, called/T79.contig-group-0.g.vcf.gz, called/M1864_2.contig-group-0.g.vcf.gz.tbi, called/M1865_2.contig-group-0.g.vcf.gz.tbi, called/M5672.contig-group-0.g.vcf.gz.tbi, called/MTDC48361.contig-group-0.g.vcf.gz.tbi, called/N2005.contig-group-0.g.vcf.gz.tbi, called/N_102.contig-group-0.g.vcf.gz.tbi, called/N_1085.contig-group-0.g.vcf.gz.tbi, called/N_1156.contig-group-0.g.vcf.gz.tbi, called/N_1157.contig-group-0.g.vcf.gz.tbi, called/N_1158.contig-group-0.g.vcf.gz.tbi, called/N_1344.contig-group-0.g.vcf.gz.tbi, called/N_1347.contig-group-0.g.vcf.gz.tbi, called/N_1354.contig-group-0.g.vcf.gz.tbi, called/N_1355.contig-group-0.g.vcf.gz.tbi, called/N_1384.contig-group-0.g.vcf.gz.tbi, called/N_1386.contig-group-0.g.vcf.gz.tbi, called/N_1390.contig-group-0.g.vcf.gz.tbi, called/N_1409.contig-group-0.g.vcf.gz.tbi, called/N_1411.contig-group-0.g.vcf.gz.tbi, called/N_1413.contig-group-0.g.vcf.gz.tbi, called/N_1414.contig-group-0.g.vcf.gz.tbi, called/N_1609.contig-group-0.g.vcf.gz.tbi, called/N_1870.contig-group-0.g.vcf.gz.tbi, called/N_1901.contig-group-0.g.vcf.gz.tbi, called/N_1913.contig-group-0.g.vcf.gz.tbi, called/N_1927.contig-group-0.g.vcf.gz.tbi, called/N_192.contig-group-0.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-0.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-0.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-0.g.vcf.gz.tbi, called/N_1992_0123.contig-group-0.g.vcf.gz.tbi, called/N_1998_0130.contig-group-0.g.vcf.gz.tbi, called/N_2001_0025.contig-group-0.g.vcf.gz.tbi, called/N_2001_0205.contig-group-0.g.vcf.gz.tbi, called/N_2002_0292.contig-group-0.g.vcf.gz.tbi, called/N_2003_5409.contig-group-0.g.vcf.gz.tbi, called/N_2004.contig-group-0.g.vcf.gz.tbi, called/N_2010_1759.contig-group-0.g.vcf.gz.tbi, called/N_21.contig-group-0.g.vcf.gz.tbi, called/N_351.contig-group-0.g.vcf.gz.tbi, called/N_355.contig-group-0.g.vcf.gz.tbi, called/N_401.contig-group-0.g.vcf.gz.tbi, called/N_403.contig-group-0.g.vcf.gz.tbi, called/N_4843.contig-group-0.g.vcf.gz.tbi, called/N_4844.contig-group-0.g.vcf.gz.tbi, called/N_4846.contig-group-0.g.vcf.gz.tbi, called/N_4847.contig-group-0.g.vcf.gz.tbi, called/N_5056.contig-group-0.g.vcf.gz.tbi, called/N_5057.contig-group-0.g.vcf.gz.tbi, called/N_5129.contig-group-0.g.vcf.gz.tbi, called/N_6489.contig-group-0.g.vcf.gz.tbi, called/N_6490.contig-group-0.g.vcf.gz.tbi, called/N_685.contig-group-0.g.vcf.gz.tbi, called/N_689.contig-group-0.g.vcf.gz.tbi, called/N_690.contig-group-0.g.vcf.gz.tbi, called/N_6926.contig-group-0.g.vcf.gz.tbi, called/N_6928.contig-group-0.g.vcf.gz.tbi, called/N_6932.contig-group-0.g.vcf.gz.tbi, called/N_6.contig-group-0.g.vcf.gz.tbi, called/N_7083.contig-group-0.g.vcf.gz.tbi, called/N_79.contig-group-0.g.vcf.gz.tbi, called/N_7.contig-group-0.g.vcf.gz.tbi, called/N_8105.contig-group-0.g.vcf.gz.tbi, called/N_8171.contig-group-0.g.vcf.gz.tbi, called/N_83.contig-group-0.g.vcf.gz.tbi, called/N_8564.contig-group-0.g.vcf.gz.tbi, called/N_8565.contig-group-0.g.vcf.gz.tbi, called/N_8583.contig-group-0.g.vcf.gz.tbi, called/N_8585.contig-group-0.g.vcf.gz.tbi, called/N_8586.contig-group-0.g.vcf.gz.tbi, called/N_9104.contig-group-0.g.vcf.gz.tbi, called/N_9449.contig-group-0.g.vcf.gz.tbi, called/N_94.contig-group-0.g.vcf.gz.tbi, called/T1481.contig-group-0.g.vcf.gz.tbi, called/T1483.contig-group-0.g.vcf.gz.tbi, called/T178.contig-group-0.g.vcf.gz.tbi, called/T179.contig-group-0.g.vcf.gz.tbi, called/T180.contig-group-0.g.vcf.gz.tbi, called/T181.contig-group-0.g.vcf.gz.tbi, called/T185.contig-group-0.g.vcf.gz.tbi, called/T186.contig-group-0.g.vcf.gz.tbi, called/T187.contig-group-0.g.vcf.gz.tbi, called/T188.contig-group-0.g.vcf.gz.tbi, called/T189.contig-group-0.g.vcf.gz.tbi, called/T190.contig-group-0.g.vcf.gz.tbi, called/T192.contig-group-0.g.vcf.gz.tbi, called/T193.contig-group-0.g.vcf.gz.tbi, called/T194.contig-group-0.g.vcf.gz.tbi, called/T196.contig-group-0.g.vcf.gz.tbi, called/T248.contig-group-0.g.vcf.gz.tbi, called/T37.contig-group-0.g.vcf.gz.tbi, called/T72.contig-group-0.g.vcf.gz.tbi, called/T79.contig-group-0.g.vcf.gz.tbi output: called/all.contig-group-0.g.vcf.gz, called/all.contig-group-0.g.done log: logs/gatk/combine-gvcfs/contig-group-0.log jobid: 1311 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-0.bench.log reason: Missing output files: called/all.contig-group-0.g.vcf.gz; Input files updated by another job: called/N_6928.contig-group-0.g.vcf.gz, called/N_690.contig-group-0.g.vcf.gz.tbi, called/N_102.contig-group-0.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-0.g.vcf.gz, called/N_83.contig-group-0.g.vcf.gz, called/N_6489.contig-group-0.g.vcf.gz.tbi, called/N_1386.contig-group-0.g.vcf.gz.tbi, called/N_8583.contig-group-0.g.vcf.gz.tbi, called/T196.contig-group-0.g.vcf.gz, called/N_689.contig-group-0.g.vcf.gz.tbi, called/N_9104.contig-group-0.g.vcf.gz, called/N_2003_5409.contig-group-0.g.vcf.gz.tbi, called/N_8171.contig-group-0.g.vcf.gz.tbi, called/N_1609.contig-group-0.g.vcf.gz.tbi, called/T1483.contig-group-0.g.vcf.gz, called/T185.contig-group-0.g.vcf.gz, called/T79.contig-group-0.g.vcf.gz, called/N_351.contig-group-0.g.vcf.gz, called/N_1354.contig-group-0.g.vcf.gz, called/T72.contig-group-0.g.vcf.gz.tbi, called/N_7.contig-group-0.g.vcf.gz, called/N_8565.contig-group-0.g.vcf.gz, called/N_1870.contig-group-0.g.vcf.gz.tbi, called/N_9449.contig-group-0.g.vcf.gz, called/N_351.contig-group-0.g.vcf.gz.tbi, called/T187.contig-group-0.g.vcf.gz.tbi, called/T192.contig-group-0.g.vcf.gz.tbi, called/N_1386.contig-group-0.g.vcf.gz, called/T196.contig-group-0.g.vcf.gz.tbi, called/N_1156.contig-group-0.g.vcf.gz.tbi, called/N_1870.contig-group-0.g.vcf.gz, called/N_4847.contig-group-0.g.vcf.gz.tbi, called/N_83.contig-group-0.g.vcf.gz.tbi, called/N_79.contig-group-0.g.vcf.gz, called/N_1934_1_1_5973.contig-group-0.g.vcf.gz.tbi, called/N_79.contig-group-0.g.vcf.gz.tbi, called/N_5129.contig-group-0.g.vcf.gz, called/N_2003_5409.contig-group-0.g.vcf.gz, called/N_6489.contig-group-0.g.vcf.gz, called/N_8565.contig-group-0.g.vcf.gz.tbi, called/N_1927.contig-group-0.g.vcf.gz.tbi, called/N_8583.contig-group-0.g.vcf.gz, called/N_1609.contig-group-0.g.vcf.gz, called/N_1157.contig-group-0.g.vcf.gz, called/M5672.contig-group-0.g.vcf.gz.tbi, called/N_6928.contig-group-0.g.vcf.gz.tbi, called/T185.contig-group-0.g.vcf.gz.tbi, called/T187.contig-group-0.g.vcf.gz, called/N_4843.contig-group-0.g.vcf.gz.tbi, called/T190.contig-group-0.g.vcf.gz, called/T190.contig-group-0.g.vcf.gz.tbi, called/N_9104.contig-group-0.g.vcf.gz.tbi, called/N_689.contig-group-0.g.vcf.gz, called/N_1156.contig-group-0.g.vcf.gz, called/N_6490.contig-group-0.g.vcf.gz.tbi, called/N_9449.contig-group-0.g.vcf.gz.tbi, called/N_1992_0123.contig-group-0.g.vcf.gz, called/N_1158.contig-group-0.g.vcf.gz, called/N_1157.contig-group-0.g.vcf.gz.tbi, called/N2005.contig-group-0.g.vcf.gz.tbi, called/N_4843.contig-group-0.g.vcf.gz, called/N_6490.contig-group-0.g.vcf.gz, called/T72.contig-group-0.g.vcf.gz, called/N_1992_0123.contig-group-0.g.vcf.gz.tbi, called/T180.contig-group-0.g.vcf.gz.tbi, called/T1483.contig-group-0.g.vcf.gz.tbi, called/M5672.contig-group-0.g.vcf.gz, called/N_5129.contig-group-0.g.vcf.gz.tbi, called/T79.contig-group-0.g.vcf.gz.tbi, called/N_690.contig-group-0.g.vcf.gz, called/N_7.contig-group-0.g.vcf.gz.tbi, called/T192.contig-group-0.g.vcf.gz, called/N_4847.contig-group-0.g.vcf.gz, called/N_8171.contig-group-0.g.vcf.gz, called/N_1158.contig-group-0.g.vcf.gz.tbi, called/N2005.contig-group-0.g.vcf.gz, called/N_102.contig-group-0.g.vcf.gz, called/N_1354.contig-group-0.g.vcf.gz.tbi, called/T180.contig-group-0.g.vcf.gz, called/N_1927.contig-group-0.g.vcf.gz wildcards: contig=contig-group-0 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-11.g.vcf.gz, called/M1865_2.contig-group-11.g.vcf.gz, called/M5672.contig-group-11.g.vcf.gz, called/MTDC48361.contig-group-11.g.vcf.gz, called/N2005.contig-group-11.g.vcf.gz, called/N_102.contig-group-11.g.vcf.gz, called/N_1085.contig-group-11.g.vcf.gz, called/N_1156.contig-group-11.g.vcf.gz, called/N_1157.contig-group-11.g.vcf.gz, called/N_1158.contig-group-11.g.vcf.gz, called/N_1344.contig-group-11.g.vcf.gz, called/N_1347.contig-group-11.g.vcf.gz, called/N_1354.contig-group-11.g.vcf.gz, called/N_1355.contig-group-11.g.vcf.gz, called/N_1384.contig-group-11.g.vcf.gz, called/N_1386.contig-group-11.g.vcf.gz, called/N_1390.contig-group-11.g.vcf.gz, called/N_1409.contig-group-11.g.vcf.gz, called/N_1411.contig-group-11.g.vcf.gz, called/N_1413.contig-group-11.g.vcf.gz, called/N_1414.contig-group-11.g.vcf.gz, called/N_1609.contig-group-11.g.vcf.gz, called/N_1870.contig-group-11.g.vcf.gz, called/N_1901.contig-group-11.g.vcf.gz, called/N_1913.contig-group-11.g.vcf.gz, called/N_1927.contig-group-11.g.vcf.gz, called/N_192.contig-group-11.g.vcf.gz, called/N_1934_1_1_368.contig-group-11.g.vcf.gz, called/N_1934_1_1_5973.contig-group-11.g.vcf.gz, called/N_1951_13_1951.contig-group-11.g.vcf.gz, called/N_1992_0123.contig-group-11.g.vcf.gz, called/N_1998_0130.contig-group-11.g.vcf.gz, called/N_2001_0025.contig-group-11.g.vcf.gz, called/N_2001_0205.contig-group-11.g.vcf.gz, called/N_2002_0292.contig-group-11.g.vcf.gz, called/N_2003_5409.contig-group-11.g.vcf.gz, called/N_2004.contig-group-11.g.vcf.gz, called/N_2010_1759.contig-group-11.g.vcf.gz, called/N_21.contig-group-11.g.vcf.gz, called/N_351.contig-group-11.g.vcf.gz, called/N_355.contig-group-11.g.vcf.gz, called/N_401.contig-group-11.g.vcf.gz, called/N_403.contig-group-11.g.vcf.gz, called/N_4843.contig-group-11.g.vcf.gz, called/N_4844.contig-group-11.g.vcf.gz, called/N_4846.contig-group-11.g.vcf.gz, called/N_4847.contig-group-11.g.vcf.gz, called/N_5056.contig-group-11.g.vcf.gz, called/N_5057.contig-group-11.g.vcf.gz, called/N_5129.contig-group-11.g.vcf.gz, called/N_6489.contig-group-11.g.vcf.gz, called/N_6490.contig-group-11.g.vcf.gz, called/N_685.contig-group-11.g.vcf.gz, called/N_689.contig-group-11.g.vcf.gz, called/N_690.contig-group-11.g.vcf.gz, called/N_6926.contig-group-11.g.vcf.gz, called/N_6928.contig-group-11.g.vcf.gz, called/N_6932.contig-group-11.g.vcf.gz, called/N_6.contig-group-11.g.vcf.gz, called/N_7083.contig-group-11.g.vcf.gz, called/N_79.contig-group-11.g.vcf.gz, called/N_7.contig-group-11.g.vcf.gz, called/N_8105.contig-group-11.g.vcf.gz, called/N_8171.contig-group-11.g.vcf.gz, called/N_83.contig-group-11.g.vcf.gz, called/N_8564.contig-group-11.g.vcf.gz, called/N_8565.contig-group-11.g.vcf.gz, called/N_8583.contig-group-11.g.vcf.gz, called/N_8585.contig-group-11.g.vcf.gz, called/N_8586.contig-group-11.g.vcf.gz, called/N_9104.contig-group-11.g.vcf.gz, called/N_9449.contig-group-11.g.vcf.gz, called/N_94.contig-group-11.g.vcf.gz, called/T1481.contig-group-11.g.vcf.gz, called/T1483.contig-group-11.g.vcf.gz, called/T178.contig-group-11.g.vcf.gz, called/T179.contig-group-11.g.vcf.gz, called/T180.contig-group-11.g.vcf.gz, called/T181.contig-group-11.g.vcf.gz, called/T185.contig-group-11.g.vcf.gz, called/T186.contig-group-11.g.vcf.gz, called/T187.contig-group-11.g.vcf.gz, called/T188.contig-group-11.g.vcf.gz, called/T189.contig-group-11.g.vcf.gz, called/T190.contig-group-11.g.vcf.gz, called/T192.contig-group-11.g.vcf.gz, called/T193.contig-group-11.g.vcf.gz, called/T194.contig-group-11.g.vcf.gz, called/T196.contig-group-11.g.vcf.gz, called/T248.contig-group-11.g.vcf.gz, called/T37.contig-group-11.g.vcf.gz, called/T72.contig-group-11.g.vcf.gz, called/T79.contig-group-11.g.vcf.gz, called/M1864_2.contig-group-11.g.vcf.gz.tbi, called/M1865_2.contig-group-11.g.vcf.gz.tbi, called/M5672.contig-group-11.g.vcf.gz.tbi, called/MTDC48361.contig-group-11.g.vcf.gz.tbi, called/N2005.contig-group-11.g.vcf.gz.tbi, called/N_102.contig-group-11.g.vcf.gz.tbi, called/N_1085.contig-group-11.g.vcf.gz.tbi, called/N_1156.contig-group-11.g.vcf.gz.tbi, called/N_1157.contig-group-11.g.vcf.gz.tbi, called/N_1158.contig-group-11.g.vcf.gz.tbi, called/N_1344.contig-group-11.g.vcf.gz.tbi, called/N_1347.contig-group-11.g.vcf.gz.tbi, called/N_1354.contig-group-11.g.vcf.gz.tbi, called/N_1355.contig-group-11.g.vcf.gz.tbi, called/N_1384.contig-group-11.g.vcf.gz.tbi, called/N_1386.contig-group-11.g.vcf.gz.tbi, called/N_1390.contig-group-11.g.vcf.gz.tbi, called/N_1409.contig-group-11.g.vcf.gz.tbi, called/N_1411.contig-group-11.g.vcf.gz.tbi, called/N_1413.contig-group-11.g.vcf.gz.tbi, called/N_1414.contig-group-11.g.vcf.gz.tbi, called/N_1609.contig-group-11.g.vcf.gz.tbi, called/N_1870.contig-group-11.g.vcf.gz.tbi, called/N_1901.contig-group-11.g.vcf.gz.tbi, called/N_1913.contig-group-11.g.vcf.gz.tbi, called/N_1927.contig-group-11.g.vcf.gz.tbi, called/N_192.contig-group-11.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-11.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-11.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-11.g.vcf.gz.tbi, called/N_1992_0123.contig-group-11.g.vcf.gz.tbi, called/N_1998_0130.contig-group-11.g.vcf.gz.tbi, called/N_2001_0025.contig-group-11.g.vcf.gz.tbi, called/N_2001_0205.contig-group-11.g.vcf.gz.tbi, called/N_2002_0292.contig-group-11.g.vcf.gz.tbi, called/N_2003_5409.contig-group-11.g.vcf.gz.tbi, called/N_2004.contig-group-11.g.vcf.gz.tbi, called/N_2010_1759.contig-group-11.g.vcf.gz.tbi, called/N_21.contig-group-11.g.vcf.gz.tbi, called/N_351.contig-group-11.g.vcf.gz.tbi, called/N_355.contig-group-11.g.vcf.gz.tbi, called/N_401.contig-group-11.g.vcf.gz.tbi, called/N_403.contig-group-11.g.vcf.gz.tbi, called/N_4843.contig-group-11.g.vcf.gz.tbi, called/N_4844.contig-group-11.g.vcf.gz.tbi, called/N_4846.contig-group-11.g.vcf.gz.tbi, called/N_4847.contig-group-11.g.vcf.gz.tbi, called/N_5056.contig-group-11.g.vcf.gz.tbi, called/N_5057.contig-group-11.g.vcf.gz.tbi, called/N_5129.contig-group-11.g.vcf.gz.tbi, called/N_6489.contig-group-11.g.vcf.gz.tbi, called/N_6490.contig-group-11.g.vcf.gz.tbi, called/N_685.contig-group-11.g.vcf.gz.tbi, called/N_689.contig-group-11.g.vcf.gz.tbi, called/N_690.contig-group-11.g.vcf.gz.tbi, called/N_6926.contig-group-11.g.vcf.gz.tbi, called/N_6928.contig-group-11.g.vcf.gz.tbi, called/N_6932.contig-group-11.g.vcf.gz.tbi, called/N_6.contig-group-11.g.vcf.gz.tbi, called/N_7083.contig-group-11.g.vcf.gz.tbi, called/N_79.contig-group-11.g.vcf.gz.tbi, called/N_7.contig-group-11.g.vcf.gz.tbi, called/N_8105.contig-group-11.g.vcf.gz.tbi, called/N_8171.contig-group-11.g.vcf.gz.tbi, called/N_83.contig-group-11.g.vcf.gz.tbi, called/N_8564.contig-group-11.g.vcf.gz.tbi, called/N_8565.contig-group-11.g.vcf.gz.tbi, called/N_8583.contig-group-11.g.vcf.gz.tbi, called/N_8585.contig-group-11.g.vcf.gz.tbi, called/N_8586.contig-group-11.g.vcf.gz.tbi, called/N_9104.contig-group-11.g.vcf.gz.tbi, called/N_9449.contig-group-11.g.vcf.gz.tbi, called/N_94.contig-group-11.g.vcf.gz.tbi, called/T1481.contig-group-11.g.vcf.gz.tbi, called/T1483.contig-group-11.g.vcf.gz.tbi, called/T178.contig-group-11.g.vcf.gz.tbi, called/T179.contig-group-11.g.vcf.gz.tbi, called/T180.contig-group-11.g.vcf.gz.tbi, called/T181.contig-group-11.g.vcf.gz.tbi, called/T185.contig-group-11.g.vcf.gz.tbi, called/T186.contig-group-11.g.vcf.gz.tbi, called/T187.contig-group-11.g.vcf.gz.tbi, called/T188.contig-group-11.g.vcf.gz.tbi, called/T189.contig-group-11.g.vcf.gz.tbi, called/T190.contig-group-11.g.vcf.gz.tbi, called/T192.contig-group-11.g.vcf.gz.tbi, called/T193.contig-group-11.g.vcf.gz.tbi, called/T194.contig-group-11.g.vcf.gz.tbi, called/T196.contig-group-11.g.vcf.gz.tbi, called/T248.contig-group-11.g.vcf.gz.tbi, called/T37.contig-group-11.g.vcf.gz.tbi, called/T72.contig-group-11.g.vcf.gz.tbi, called/T79.contig-group-11.g.vcf.gz.tbi output: called/all.contig-group-11.g.vcf.gz, called/all.contig-group-11.g.done log: logs/gatk/combine-gvcfs/contig-group-11.log jobid: 2461 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-11.bench.log reason: Input files updated by another job: called/N_6490.contig-group-11.g.vcf.gz, called/N_1992_0123.contig-group-11.g.vcf.gz, called/N_5129.contig-group-11.g.vcf.gz, called/N_689.contig-group-11.g.vcf.gz.tbi, called/T180.contig-group-11.g.vcf.gz, called/N_1870.contig-group-11.g.vcf.gz.tbi, called/N_351.contig-group-11.g.vcf.gz.tbi, called/T187.contig-group-11.g.vcf.gz, called/N_6928.contig-group-11.g.vcf.gz, called/N_1157.contig-group-11.g.vcf.gz.tbi, called/T196.contig-group-11.g.vcf.gz, called/M5672.contig-group-11.g.vcf.gz, called/T180.contig-group-11.g.vcf.gz.tbi, called/N_1992_0123.contig-group-11.g.vcf.gz.tbi, called/N_6928.contig-group-11.g.vcf.gz.tbi, called/N_79.contig-group-11.g.vcf.gz.tbi, called/N_1156.contig-group-11.g.vcf.gz, called/N_1386.contig-group-11.g.vcf.gz, called/N_5129.contig-group-11.g.vcf.gz.tbi, called/T187.contig-group-11.g.vcf.gz.tbi, called/N_4847.contig-group-11.g.vcf.gz, called/N_4847.contig-group-11.g.vcf.gz.tbi, called/N_4843.contig-group-11.g.vcf.gz, called/N_6489.contig-group-11.g.vcf.gz, called/N2005.contig-group-11.g.vcf.gz.tbi, called/N_9449.contig-group-11.g.vcf.gz.tbi, called/N_1354.contig-group-11.g.vcf.gz.tbi, called/N_83.contig-group-11.g.vcf.gz.tbi, called/N_8583.contig-group-11.g.vcf.gz, called/N_1158.contig-group-11.g.vcf.gz.tbi, called/N_1158.contig-group-11.g.vcf.gz, called/N_690.contig-group-11.g.vcf.gz.tbi, called/N_1927.contig-group-11.g.vcf.gz.tbi, called/N_1386.contig-group-11.g.vcf.gz.tbi, called/N_83.contig-group-11.g.vcf.gz, called/N_1609.contig-group-11.g.vcf.gz.tbi, called/T72.contig-group-11.g.vcf.gz.tbi, called/T192.contig-group-11.g.vcf.gz.tbi, called/N_689.contig-group-11.g.vcf.gz, called/N_4843.contig-group-11.g.vcf.gz.tbi, called/N_1870.contig-group-11.g.vcf.gz, called/N_1934_1_1_5973.contig-group-11.g.vcf.gz.tbi, called/T72.contig-group-11.g.vcf.gz, called/N_1609.contig-group-11.g.vcf.gz, called/N_6490.contig-group-11.g.vcf.gz.tbi, called/N_6489.contig-group-11.g.vcf.gz.tbi, called/N_8565.contig-group-11.g.vcf.gz.tbi, called/N_1156.contig-group-11.g.vcf.gz.tbi, called/N_8171.contig-group-11.g.vcf.gz, called/T185.contig-group-11.g.vcf.gz, called/T190.contig-group-11.g.vcf.gz, called/T79.contig-group-11.g.vcf.gz, called/N_79.contig-group-11.g.vcf.gz, called/N_9449.contig-group-11.g.vcf.gz, called/T79.contig-group-11.g.vcf.gz.tbi, called/N_102.contig-group-11.g.vcf.gz, called/N_1934_1_1_5973.contig-group-11.g.vcf.gz, called/N_351.contig-group-11.g.vcf.gz, called/N_8583.contig-group-11.g.vcf.gz.tbi, called/N_8171.contig-group-11.g.vcf.gz.tbi, called/N_1354.contig-group-11.g.vcf.gz, called/N_690.contig-group-11.g.vcf.gz, called/N_2003_5409.contig-group-11.g.vcf.gz.tbi, called/N2005.contig-group-11.g.vcf.gz, called/T1483.contig-group-11.g.vcf.gz.tbi, called/T192.contig-group-11.g.vcf.gz, called/N_1157.contig-group-11.g.vcf.gz, called/N_9104.contig-group-11.g.vcf.gz, called/N_102.contig-group-11.g.vcf.gz.tbi, called/N_9104.contig-group-11.g.vcf.gz.tbi, called/N_2003_5409.contig-group-11.g.vcf.gz, called/N_1927.contig-group-11.g.vcf.gz, called/N_8565.contig-group-11.g.vcf.gz, called/M5672.contig-group-11.g.vcf.gz.tbi, called/T1483.contig-group-11.g.vcf.gz, called/T190.contig-group-11.g.vcf.gz.tbi, called/T196.contig-group-11.g.vcf.gz.tbi, called/T185.contig-group-11.g.vcf.gz.tbi wildcards: contig=contig-group-11 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-18.g.vcf.gz, called/M1865_2.contig-group-18.g.vcf.gz, called/M5672.contig-group-18.g.vcf.gz, called/MTDC48361.contig-group-18.g.vcf.gz, called/N2005.contig-group-18.g.vcf.gz, called/N_102.contig-group-18.g.vcf.gz, called/N_1085.contig-group-18.g.vcf.gz, called/N_1156.contig-group-18.g.vcf.gz, called/N_1157.contig-group-18.g.vcf.gz, called/N_1158.contig-group-18.g.vcf.gz, called/N_1344.contig-group-18.g.vcf.gz, called/N_1347.contig-group-18.g.vcf.gz, called/N_1354.contig-group-18.g.vcf.gz, called/N_1355.contig-group-18.g.vcf.gz, called/N_1384.contig-group-18.g.vcf.gz, called/N_1386.contig-group-18.g.vcf.gz, called/N_1390.contig-group-18.g.vcf.gz, called/N_1409.contig-group-18.g.vcf.gz, called/N_1411.contig-group-18.g.vcf.gz, called/N_1413.contig-group-18.g.vcf.gz, called/N_1414.contig-group-18.g.vcf.gz, called/N_1609.contig-group-18.g.vcf.gz, called/N_1870.contig-group-18.g.vcf.gz, called/N_1901.contig-group-18.g.vcf.gz, called/N_1913.contig-group-18.g.vcf.gz, called/N_1927.contig-group-18.g.vcf.gz, called/N_192.contig-group-18.g.vcf.gz, called/N_1934_1_1_368.contig-group-18.g.vcf.gz, called/N_1934_1_1_5973.contig-group-18.g.vcf.gz, called/N_1951_13_1951.contig-group-18.g.vcf.gz, called/N_1992_0123.contig-group-18.g.vcf.gz, called/N_1998_0130.contig-group-18.g.vcf.gz, called/N_2001_0025.contig-group-18.g.vcf.gz, called/N_2001_0205.contig-group-18.g.vcf.gz, called/N_2002_0292.contig-group-18.g.vcf.gz, called/N_2003_5409.contig-group-18.g.vcf.gz, called/N_2004.contig-group-18.g.vcf.gz, called/N_2010_1759.contig-group-18.g.vcf.gz, called/N_21.contig-group-18.g.vcf.gz, called/N_351.contig-group-18.g.vcf.gz, called/N_355.contig-group-18.g.vcf.gz, called/N_401.contig-group-18.g.vcf.gz, called/N_403.contig-group-18.g.vcf.gz, called/N_4843.contig-group-18.g.vcf.gz, called/N_4844.contig-group-18.g.vcf.gz, called/N_4846.contig-group-18.g.vcf.gz, called/N_4847.contig-group-18.g.vcf.gz, called/N_5056.contig-group-18.g.vcf.gz, called/N_5057.contig-group-18.g.vcf.gz, called/N_5129.contig-group-18.g.vcf.gz, called/N_6489.contig-group-18.g.vcf.gz, called/N_6490.contig-group-18.g.vcf.gz, called/N_685.contig-group-18.g.vcf.gz, called/N_689.contig-group-18.g.vcf.gz, called/N_690.contig-group-18.g.vcf.gz, called/N_6926.contig-group-18.g.vcf.gz, called/N_6928.contig-group-18.g.vcf.gz, called/N_6932.contig-group-18.g.vcf.gz, called/N_6.contig-group-18.g.vcf.gz, called/N_7083.contig-group-18.g.vcf.gz, called/N_79.contig-group-18.g.vcf.gz, called/N_7.contig-group-18.g.vcf.gz, called/N_8105.contig-group-18.g.vcf.gz, called/N_8171.contig-group-18.g.vcf.gz, called/N_83.contig-group-18.g.vcf.gz, called/N_8564.contig-group-18.g.vcf.gz, called/N_8565.contig-group-18.g.vcf.gz, called/N_8583.contig-group-18.g.vcf.gz, called/N_8585.contig-group-18.g.vcf.gz, called/N_8586.contig-group-18.g.vcf.gz, called/N_9104.contig-group-18.g.vcf.gz, called/N_9449.contig-group-18.g.vcf.gz, called/N_94.contig-group-18.g.vcf.gz, called/T1481.contig-group-18.g.vcf.gz, called/T1483.contig-group-18.g.vcf.gz, called/T178.contig-group-18.g.vcf.gz, called/T179.contig-group-18.g.vcf.gz, called/T180.contig-group-18.g.vcf.gz, called/T181.contig-group-18.g.vcf.gz, called/T185.contig-group-18.g.vcf.gz, called/T186.contig-group-18.g.vcf.gz, called/T187.contig-group-18.g.vcf.gz, called/T188.contig-group-18.g.vcf.gz, called/T189.contig-group-18.g.vcf.gz, called/T190.contig-group-18.g.vcf.gz, called/T192.contig-group-18.g.vcf.gz, called/T193.contig-group-18.g.vcf.gz, called/T194.contig-group-18.g.vcf.gz, called/T196.contig-group-18.g.vcf.gz, called/T248.contig-group-18.g.vcf.gz, called/T37.contig-group-18.g.vcf.gz, called/T72.contig-group-18.g.vcf.gz, called/T79.contig-group-18.g.vcf.gz, called/M1864_2.contig-group-18.g.vcf.gz.tbi, called/M1865_2.contig-group-18.g.vcf.gz.tbi, called/M5672.contig-group-18.g.vcf.gz.tbi, called/MTDC48361.contig-group-18.g.vcf.gz.tbi, called/N2005.contig-group-18.g.vcf.gz.tbi, called/N_102.contig-group-18.g.vcf.gz.tbi, called/N_1085.contig-group-18.g.vcf.gz.tbi, called/N_1156.contig-group-18.g.vcf.gz.tbi, called/N_1157.contig-group-18.g.vcf.gz.tbi, called/N_1158.contig-group-18.g.vcf.gz.tbi, called/N_1344.contig-group-18.g.vcf.gz.tbi, called/N_1347.contig-group-18.g.vcf.gz.tbi, called/N_1354.contig-group-18.g.vcf.gz.tbi, called/N_1355.contig-group-18.g.vcf.gz.tbi, called/N_1384.contig-group-18.g.vcf.gz.tbi, called/N_1386.contig-group-18.g.vcf.gz.tbi, called/N_1390.contig-group-18.g.vcf.gz.tbi, called/N_1409.contig-group-18.g.vcf.gz.tbi, called/N_1411.contig-group-18.g.vcf.gz.tbi, called/N_1413.contig-group-18.g.vcf.gz.tbi, called/N_1414.contig-group-18.g.vcf.gz.tbi, called/N_1609.contig-group-18.g.vcf.gz.tbi, called/N_1870.contig-group-18.g.vcf.gz.tbi, called/N_1901.contig-group-18.g.vcf.gz.tbi, called/N_1913.contig-group-18.g.vcf.gz.tbi, called/N_1927.contig-group-18.g.vcf.gz.tbi, called/N_192.contig-group-18.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-18.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-18.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-18.g.vcf.gz.tbi, called/N_1992_0123.contig-group-18.g.vcf.gz.tbi, called/N_1998_0130.contig-group-18.g.vcf.gz.tbi, called/N_2001_0025.contig-group-18.g.vcf.gz.tbi, called/N_2001_0205.contig-group-18.g.vcf.gz.tbi, called/N_2002_0292.contig-group-18.g.vcf.gz.tbi, called/N_2003_5409.contig-group-18.g.vcf.gz.tbi, called/N_2004.contig-group-18.g.vcf.gz.tbi, called/N_2010_1759.contig-group-18.g.vcf.gz.tbi, called/N_21.contig-group-18.g.vcf.gz.tbi, called/N_351.contig-group-18.g.vcf.gz.tbi, called/N_355.contig-group-18.g.vcf.gz.tbi, called/N_401.contig-group-18.g.vcf.gz.tbi, called/N_403.contig-group-18.g.vcf.gz.tbi, called/N_4843.contig-group-18.g.vcf.gz.tbi, called/N_4844.contig-group-18.g.vcf.gz.tbi, called/N_4846.contig-group-18.g.vcf.gz.tbi, called/N_4847.contig-group-18.g.vcf.gz.tbi, called/N_5056.contig-group-18.g.vcf.gz.tbi, called/N_5057.contig-group-18.g.vcf.gz.tbi, called/N_5129.contig-group-18.g.vcf.gz.tbi, called/N_6489.contig-group-18.g.vcf.gz.tbi, called/N_6490.contig-group-18.g.vcf.gz.tbi, called/N_685.contig-group-18.g.vcf.gz.tbi, called/N_689.contig-group-18.g.vcf.gz.tbi, called/N_690.contig-group-18.g.vcf.gz.tbi, called/N_6926.contig-group-18.g.vcf.gz.tbi, called/N_6928.contig-group-18.g.vcf.gz.tbi, called/N_6932.contig-group-18.g.vcf.gz.tbi, called/N_6.contig-group-18.g.vcf.gz.tbi, called/N_7083.contig-group-18.g.vcf.gz.tbi, called/N_79.contig-group-18.g.vcf.gz.tbi, called/N_7.contig-group-18.g.vcf.gz.tbi, called/N_8105.contig-group-18.g.vcf.gz.tbi, called/N_8171.contig-group-18.g.vcf.gz.tbi, called/N_83.contig-group-18.g.vcf.gz.tbi, called/N_8564.contig-group-18.g.vcf.gz.tbi, called/N_8565.contig-group-18.g.vcf.gz.tbi, called/N_8583.contig-group-18.g.vcf.gz.tbi, called/N_8585.contig-group-18.g.vcf.gz.tbi, called/N_8586.contig-group-18.g.vcf.gz.tbi, called/N_9104.contig-group-18.g.vcf.gz.tbi, called/N_9449.contig-group-18.g.vcf.gz.tbi, called/N_94.contig-group-18.g.vcf.gz.tbi, called/T1481.contig-group-18.g.vcf.gz.tbi, called/T1483.contig-group-18.g.vcf.gz.tbi, called/T178.contig-group-18.g.vcf.gz.tbi, called/T179.contig-group-18.g.vcf.gz.tbi, called/T180.contig-group-18.g.vcf.gz.tbi, called/T181.contig-group-18.g.vcf.gz.tbi, called/T185.contig-group-18.g.vcf.gz.tbi, called/T186.contig-group-18.g.vcf.gz.tbi, called/T187.contig-group-18.g.vcf.gz.tbi, called/T188.contig-group-18.g.vcf.gz.tbi, called/T189.contig-group-18.g.vcf.gz.tbi, called/T190.contig-group-18.g.vcf.gz.tbi, called/T192.contig-group-18.g.vcf.gz.tbi, called/T193.contig-group-18.g.vcf.gz.tbi, called/T194.contig-group-18.g.vcf.gz.tbi, called/T196.contig-group-18.g.vcf.gz.tbi, called/T248.contig-group-18.g.vcf.gz.tbi, called/T37.contig-group-18.g.vcf.gz.tbi, called/T72.contig-group-18.g.vcf.gz.tbi, called/T79.contig-group-18.g.vcf.gz.tbi output: called/all.contig-group-18.g.vcf.gz, called/all.contig-group-18.g.done log: logs/gatk/combine-gvcfs/contig-group-18.log jobid: 3133 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-18.bench.log reason: Input files updated by another job: called/N_1934_1_1_5973.contig-group-18.g.vcf.gz, called/T180.contig-group-18.g.vcf.gz.tbi, called/T72.contig-group-18.g.vcf.gz.tbi, called/N_4847.contig-group-18.g.vcf.gz.tbi, called/N_1354.contig-group-18.g.vcf.gz, called/N_1992_0123.contig-group-18.g.vcf.gz, called/T185.contig-group-18.g.vcf.gz.tbi, called/N_102.contig-group-18.g.vcf.gz.tbi, called/T1483.contig-group-18.g.vcf.gz.tbi, called/M5672.contig-group-18.g.vcf.gz.tbi, called/N_9104.contig-group-18.g.vcf.gz.tbi, called/N_1927.contig-group-18.g.vcf.gz, called/N_6489.contig-group-18.g.vcf.gz, called/N_83.contig-group-18.g.vcf.gz, called/N_1157.contig-group-18.g.vcf.gz.tbi, called/N_1386.contig-group-18.g.vcf.gz, called/T185.contig-group-18.g.vcf.gz, called/M5672.contig-group-18.g.vcf.gz, called/T196.contig-group-18.g.vcf.gz, called/N_6490.contig-group-18.g.vcf.gz, called/N_4847.contig-group-18.g.vcf.gz, called/T192.contig-group-18.g.vcf.gz, called/N_102.contig-group-18.g.vcf.gz, called/N_1158.contig-group-18.g.vcf.gz, called/N_1609.contig-group-18.g.vcf.gz, called/N_351.contig-group-18.g.vcf.gz.tbi, called/N_8171.contig-group-18.g.vcf.gz.tbi, called/T180.contig-group-18.g.vcf.gz, called/N_4843.contig-group-18.g.vcf.gz, called/N_79.contig-group-18.g.vcf.gz, called/N2005.contig-group-18.g.vcf.gz.tbi, called/N_9449.contig-group-18.g.vcf.gz.tbi, called/N_6489.contig-group-18.g.vcf.gz.tbi, called/T187.contig-group-18.g.vcf.gz, called/N_1157.contig-group-18.g.vcf.gz, called/N_4843.contig-group-18.g.vcf.gz.tbi, called/N_1158.contig-group-18.g.vcf.gz.tbi, called/T187.contig-group-18.g.vcf.gz.tbi, called/T79.contig-group-18.g.vcf.gz.tbi, called/N_79.contig-group-18.g.vcf.gz.tbi, called/N_9104.contig-group-18.g.vcf.gz, called/N_8583.contig-group-18.g.vcf.gz.tbi, called/N_5129.contig-group-18.g.vcf.gz, called/N_8565.contig-group-18.g.vcf.gz.tbi, called/N_8171.contig-group-18.g.vcf.gz, called/N_351.contig-group-18.g.vcf.gz, called/N_5129.contig-group-18.g.vcf.gz.tbi, called/N_8565.contig-group-18.g.vcf.gz, called/T79.contig-group-18.g.vcf.gz, called/N_1934_1_1_5973.contig-group-18.g.vcf.gz.tbi, called/N_689.contig-group-18.g.vcf.gz.tbi, called/N_2003_5409.contig-group-18.g.vcf.gz, called/N_2003_5409.contig-group-18.g.vcf.gz.tbi, called/N_690.contig-group-18.g.vcf.gz.tbi, called/N_6928.contig-group-18.g.vcf.gz, called/T1483.contig-group-18.g.vcf.gz, called/N_1156.contig-group-18.g.vcf.gz, called/N_1386.contig-group-18.g.vcf.gz.tbi, called/N_1992_0123.contig-group-18.g.vcf.gz.tbi, called/T192.contig-group-18.g.vcf.gz.tbi, called/N_690.contig-group-18.g.vcf.gz, called/N_6928.contig-group-18.g.vcf.gz.tbi, called/N_9449.contig-group-18.g.vcf.gz, called/N_1927.contig-group-18.g.vcf.gz.tbi, called/N_1156.contig-group-18.g.vcf.gz.tbi, called/N_1354.contig-group-18.g.vcf.gz.tbi, called/T190.contig-group-18.g.vcf.gz, called/N_689.contig-group-18.g.vcf.gz, called/T72.contig-group-18.g.vcf.gz, called/N_1609.contig-group-18.g.vcf.gz.tbi, called/N2005.contig-group-18.g.vcf.gz, called/N_1870.contig-group-18.g.vcf.gz, called/T190.contig-group-18.g.vcf.gz.tbi, called/N_6490.contig-group-18.g.vcf.gz.tbi, called/N_8583.contig-group-18.g.vcf.gz, called/N_83.contig-group-18.g.vcf.gz.tbi, called/N_1870.contig-group-18.g.vcf.gz.tbi, called/T196.contig-group-18.g.vcf.gz.tbi wildcards: contig=contig-group-18 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-20.g.vcf.gz, called/M1865_2.contig-group-20.g.vcf.gz, called/M5672.contig-group-20.g.vcf.gz, called/MTDC48361.contig-group-20.g.vcf.gz, called/N2005.contig-group-20.g.vcf.gz, called/N_102.contig-group-20.g.vcf.gz, called/N_1085.contig-group-20.g.vcf.gz, called/N_1156.contig-group-20.g.vcf.gz, called/N_1157.contig-group-20.g.vcf.gz, called/N_1158.contig-group-20.g.vcf.gz, called/N_1344.contig-group-20.g.vcf.gz, called/N_1347.contig-group-20.g.vcf.gz, called/N_1354.contig-group-20.g.vcf.gz, called/N_1355.contig-group-20.g.vcf.gz, called/N_1384.contig-group-20.g.vcf.gz, called/N_1386.contig-group-20.g.vcf.gz, called/N_1390.contig-group-20.g.vcf.gz, called/N_1409.contig-group-20.g.vcf.gz, called/N_1411.contig-group-20.g.vcf.gz, called/N_1413.contig-group-20.g.vcf.gz, called/N_1414.contig-group-20.g.vcf.gz, called/N_1609.contig-group-20.g.vcf.gz, called/N_1870.contig-group-20.g.vcf.gz, called/N_1901.contig-group-20.g.vcf.gz, called/N_1913.contig-group-20.g.vcf.gz, called/N_1927.contig-group-20.g.vcf.gz, called/N_192.contig-group-20.g.vcf.gz, called/N_1934_1_1_368.contig-group-20.g.vcf.gz, called/N_1934_1_1_5973.contig-group-20.g.vcf.gz, called/N_1951_13_1951.contig-group-20.g.vcf.gz, called/N_1992_0123.contig-group-20.g.vcf.gz, called/N_1998_0130.contig-group-20.g.vcf.gz, called/N_2001_0025.contig-group-20.g.vcf.gz, called/N_2001_0205.contig-group-20.g.vcf.gz, called/N_2002_0292.contig-group-20.g.vcf.gz, called/N_2003_5409.contig-group-20.g.vcf.gz, called/N_2004.contig-group-20.g.vcf.gz, called/N_2010_1759.contig-group-20.g.vcf.gz, called/N_21.contig-group-20.g.vcf.gz, called/N_351.contig-group-20.g.vcf.gz, called/N_355.contig-group-20.g.vcf.gz, called/N_401.contig-group-20.g.vcf.gz, called/N_403.contig-group-20.g.vcf.gz, called/N_4843.contig-group-20.g.vcf.gz, called/N_4844.contig-group-20.g.vcf.gz, called/N_4846.contig-group-20.g.vcf.gz, called/N_4847.contig-group-20.g.vcf.gz, called/N_5056.contig-group-20.g.vcf.gz, called/N_5057.contig-group-20.g.vcf.gz, called/N_5129.contig-group-20.g.vcf.gz, called/N_6489.contig-group-20.g.vcf.gz, called/N_6490.contig-group-20.g.vcf.gz, called/N_685.contig-group-20.g.vcf.gz, called/N_689.contig-group-20.g.vcf.gz, called/N_690.contig-group-20.g.vcf.gz, called/N_6926.contig-group-20.g.vcf.gz, called/N_6928.contig-group-20.g.vcf.gz, called/N_6932.contig-group-20.g.vcf.gz, called/N_6.contig-group-20.g.vcf.gz, called/N_7083.contig-group-20.g.vcf.gz, called/N_79.contig-group-20.g.vcf.gz, called/N_7.contig-group-20.g.vcf.gz, called/N_8105.contig-group-20.g.vcf.gz, called/N_8171.contig-group-20.g.vcf.gz, called/N_83.contig-group-20.g.vcf.gz, called/N_8564.contig-group-20.g.vcf.gz, called/N_8565.contig-group-20.g.vcf.gz, called/N_8583.contig-group-20.g.vcf.gz, called/N_8585.contig-group-20.g.vcf.gz, called/N_8586.contig-group-20.g.vcf.gz, called/N_9104.contig-group-20.g.vcf.gz, called/N_9449.contig-group-20.g.vcf.gz, called/N_94.contig-group-20.g.vcf.gz, called/T1481.contig-group-20.g.vcf.gz, called/T1483.contig-group-20.g.vcf.gz, called/T178.contig-group-20.g.vcf.gz, called/T179.contig-group-20.g.vcf.gz, called/T180.contig-group-20.g.vcf.gz, called/T181.contig-group-20.g.vcf.gz, called/T185.contig-group-20.g.vcf.gz, called/T186.contig-group-20.g.vcf.gz, called/T187.contig-group-20.g.vcf.gz, called/T188.contig-group-20.g.vcf.gz, called/T189.contig-group-20.g.vcf.gz, called/T190.contig-group-20.g.vcf.gz, called/T192.contig-group-20.g.vcf.gz, called/T193.contig-group-20.g.vcf.gz, called/T194.contig-group-20.g.vcf.gz, called/T196.contig-group-20.g.vcf.gz, called/T248.contig-group-20.g.vcf.gz, called/T37.contig-group-20.g.vcf.gz, called/T72.contig-group-20.g.vcf.gz, called/T79.contig-group-20.g.vcf.gz, called/M1864_2.contig-group-20.g.vcf.gz.tbi, called/M1865_2.contig-group-20.g.vcf.gz.tbi, called/M5672.contig-group-20.g.vcf.gz.tbi, called/MTDC48361.contig-group-20.g.vcf.gz.tbi, called/N2005.contig-group-20.g.vcf.gz.tbi, called/N_102.contig-group-20.g.vcf.gz.tbi, called/N_1085.contig-group-20.g.vcf.gz.tbi, called/N_1156.contig-group-20.g.vcf.gz.tbi, called/N_1157.contig-group-20.g.vcf.gz.tbi, called/N_1158.contig-group-20.g.vcf.gz.tbi, called/N_1344.contig-group-20.g.vcf.gz.tbi, called/N_1347.contig-group-20.g.vcf.gz.tbi, called/N_1354.contig-group-20.g.vcf.gz.tbi, called/N_1355.contig-group-20.g.vcf.gz.tbi, called/N_1384.contig-group-20.g.vcf.gz.tbi, called/N_1386.contig-group-20.g.vcf.gz.tbi, called/N_1390.contig-group-20.g.vcf.gz.tbi, called/N_1409.contig-group-20.g.vcf.gz.tbi, called/N_1411.contig-group-20.g.vcf.gz.tbi, called/N_1413.contig-group-20.g.vcf.gz.tbi, called/N_1414.contig-group-20.g.vcf.gz.tbi, called/N_1609.contig-group-20.g.vcf.gz.tbi, called/N_1870.contig-group-20.g.vcf.gz.tbi, called/N_1901.contig-group-20.g.vcf.gz.tbi, called/N_1913.contig-group-20.g.vcf.gz.tbi, called/N_1927.contig-group-20.g.vcf.gz.tbi, called/N_192.contig-group-20.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-20.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-20.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-20.g.vcf.gz.tbi, called/N_1992_0123.contig-group-20.g.vcf.gz.tbi, called/N_1998_0130.contig-group-20.g.vcf.gz.tbi, called/N_2001_0025.contig-group-20.g.vcf.gz.tbi, called/N_2001_0205.contig-group-20.g.vcf.gz.tbi, called/N_2002_0292.contig-group-20.g.vcf.gz.tbi, called/N_2003_5409.contig-group-20.g.vcf.gz.tbi, called/N_2004.contig-group-20.g.vcf.gz.tbi, called/N_2010_1759.contig-group-20.g.vcf.gz.tbi, called/N_21.contig-group-20.g.vcf.gz.tbi, called/N_351.contig-group-20.g.vcf.gz.tbi, called/N_355.contig-group-20.g.vcf.gz.tbi, called/N_401.contig-group-20.g.vcf.gz.tbi, called/N_403.contig-group-20.g.vcf.gz.tbi, called/N_4843.contig-group-20.g.vcf.gz.tbi, called/N_4844.contig-group-20.g.vcf.gz.tbi, called/N_4846.contig-group-20.g.vcf.gz.tbi, called/N_4847.contig-group-20.g.vcf.gz.tbi, called/N_5056.contig-group-20.g.vcf.gz.tbi, called/N_5057.contig-group-20.g.vcf.gz.tbi, called/N_5129.contig-group-20.g.vcf.gz.tbi, called/N_6489.contig-group-20.g.vcf.gz.tbi, called/N_6490.contig-group-20.g.vcf.gz.tbi, called/N_685.contig-group-20.g.vcf.gz.tbi, called/N_689.contig-group-20.g.vcf.gz.tbi, called/N_690.contig-group-20.g.vcf.gz.tbi, called/N_6926.contig-group-20.g.vcf.gz.tbi, called/N_6928.contig-group-20.g.vcf.gz.tbi, called/N_6932.contig-group-20.g.vcf.gz.tbi, called/N_6.contig-group-20.g.vcf.gz.tbi, called/N_7083.contig-group-20.g.vcf.gz.tbi, called/N_79.contig-group-20.g.vcf.gz.tbi, called/N_7.contig-group-20.g.vcf.gz.tbi, called/N_8105.contig-group-20.g.vcf.gz.tbi, called/N_8171.contig-group-20.g.vcf.gz.tbi, called/N_83.contig-group-20.g.vcf.gz.tbi, called/N_8564.contig-group-20.g.vcf.gz.tbi, called/N_8565.contig-group-20.g.vcf.gz.tbi, called/N_8583.contig-group-20.g.vcf.gz.tbi, called/N_8585.contig-group-20.g.vcf.gz.tbi, called/N_8586.contig-group-20.g.vcf.gz.tbi, called/N_9104.contig-group-20.g.vcf.gz.tbi, called/N_9449.contig-group-20.g.vcf.gz.tbi, called/N_94.contig-group-20.g.vcf.gz.tbi, called/T1481.contig-group-20.g.vcf.gz.tbi, called/T1483.contig-group-20.g.vcf.gz.tbi, called/T178.contig-group-20.g.vcf.gz.tbi, called/T179.contig-group-20.g.vcf.gz.tbi, called/T180.contig-group-20.g.vcf.gz.tbi, called/T181.contig-group-20.g.vcf.gz.tbi, called/T185.contig-group-20.g.vcf.gz.tbi, called/T186.contig-group-20.g.vcf.gz.tbi, called/T187.contig-group-20.g.vcf.gz.tbi, called/T188.contig-group-20.g.vcf.gz.tbi, called/T189.contig-group-20.g.vcf.gz.tbi, called/T190.contig-group-20.g.vcf.gz.tbi, called/T192.contig-group-20.g.vcf.gz.tbi, called/T193.contig-group-20.g.vcf.gz.tbi, called/T194.contig-group-20.g.vcf.gz.tbi, called/T196.contig-group-20.g.vcf.gz.tbi, called/T248.contig-group-20.g.vcf.gz.tbi, called/T37.contig-group-20.g.vcf.gz.tbi, called/T72.contig-group-20.g.vcf.gz.tbi, called/T79.contig-group-20.g.vcf.gz.tbi output: called/all.contig-group-20.g.vcf.gz, called/all.contig-group-20.g.done log: logs/gatk/combine-gvcfs/contig-group-20.log jobid: 3325 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-20.bench.log reason: Input files updated by another job: called/N_5129.contig-group-20.g.vcf.gz.tbi, called/N_102.contig-group-20.g.vcf.gz.tbi, called/N_2003_5409.contig-group-20.g.vcf.gz.tbi, called/N_1157.contig-group-20.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-20.g.vcf.gz, called/N_1158.contig-group-20.g.vcf.gz.tbi, called/N_689.contig-group-20.g.vcf.gz, called/N_79.contig-group-20.g.vcf.gz, called/N_9449.contig-group-20.g.vcf.gz, called/T190.contig-group-20.g.vcf.gz, called/N_8583.contig-group-20.g.vcf.gz.tbi, called/N_1609.contig-group-20.g.vcf.gz, called/N_1992_0123.contig-group-20.g.vcf.gz, called/N_9104.contig-group-20.g.vcf.gz, called/N_1927.contig-group-20.g.vcf.gz.tbi, called/N_8171.contig-group-20.g.vcf.gz.tbi, called/M5672.contig-group-20.g.vcf.gz.tbi, called/N_689.contig-group-20.g.vcf.gz.tbi, called/N_5129.contig-group-20.g.vcf.gz, called/N_1354.contig-group-20.g.vcf.gz.tbi, called/N_690.contig-group-20.g.vcf.gz, called/N_8565.contig-group-20.g.vcf.gz, called/N_102.contig-group-20.g.vcf.gz, called/N_6928.contig-group-20.g.vcf.gz, called/N_690.contig-group-20.g.vcf.gz.tbi, called/N_83.contig-group-20.g.vcf.gz, called/N_1386.contig-group-20.g.vcf.gz.tbi, called/T1483.contig-group-20.g.vcf.gz, called/T196.contig-group-20.g.vcf.gz, called/N_1870.contig-group-20.g.vcf.gz.tbi, called/N_6489.contig-group-20.g.vcf.gz, called/M5672.contig-group-20.g.vcf.gz, called/N_6490.contig-group-20.g.vcf.gz, called/N_351.contig-group-20.g.vcf.gz, called/N_1157.contig-group-20.g.vcf.gz, called/N_1354.contig-group-20.g.vcf.gz, called/N_9449.contig-group-20.g.vcf.gz.tbi, called/N_1870.contig-group-20.g.vcf.gz, called/T72.contig-group-20.g.vcf.gz.tbi, called/T196.contig-group-20.g.vcf.gz.tbi, called/T192.contig-group-20.g.vcf.gz, called/T72.contig-group-20.g.vcf.gz, called/N_9104.contig-group-20.g.vcf.gz.tbi, called/N_1386.contig-group-20.g.vcf.gz, called/T187.contig-group-20.g.vcf.gz.tbi, called/N_6489.contig-group-20.g.vcf.gz.tbi, called/T180.contig-group-20.g.vcf.gz.tbi, called/N_8583.contig-group-20.g.vcf.gz, called/T1483.contig-group-20.g.vcf.gz.tbi, called/N_1609.contig-group-20.g.vcf.gz.tbi, called/T79.contig-group-20.g.vcf.gz, called/N2005.contig-group-20.g.vcf.gz, called/N_2003_5409.contig-group-20.g.vcf.gz, called/N_4843.contig-group-20.g.vcf.gz.tbi, called/N_1158.contig-group-20.g.vcf.gz, called/N2005.contig-group-20.g.vcf.gz.tbi, called/N_79.contig-group-20.g.vcf.gz.tbi, called/N_6928.contig-group-20.g.vcf.gz.tbi, called/N_1927.contig-group-20.g.vcf.gz, called/N_8565.contig-group-20.g.vcf.gz.tbi, called/N_4847.contig-group-20.g.vcf.gz.tbi, called/N_6490.contig-group-20.g.vcf.gz.tbi, called/N_4843.contig-group-20.g.vcf.gz, called/N_1156.contig-group-20.g.vcf.gz, called/T185.contig-group-20.g.vcf.gz, called/N_1992_0123.contig-group-20.g.vcf.gz.tbi, called/T180.contig-group-20.g.vcf.gz, called/N_1156.contig-group-20.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-20.g.vcf.gz.tbi, called/N_351.contig-group-20.g.vcf.gz.tbi, called/N_4847.contig-group-20.g.vcf.gz, called/T185.contig-group-20.g.vcf.gz.tbi, called/T190.contig-group-20.g.vcf.gz.tbi, called/T192.contig-group-20.g.vcf.gz.tbi, called/N_8171.contig-group-20.g.vcf.gz, called/N_83.contig-group-20.g.vcf.gz.tbi, called/T79.contig-group-20.g.vcf.gz.tbi, called/T187.contig-group-20.g.vcf.gz wildcards: contig=contig-group-20 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-16.g.vcf.gz, called/M1865_2.contig-group-16.g.vcf.gz, called/M5672.contig-group-16.g.vcf.gz, called/MTDC48361.contig-group-16.g.vcf.gz, called/N2005.contig-group-16.g.vcf.gz, called/N_102.contig-group-16.g.vcf.gz, called/N_1085.contig-group-16.g.vcf.gz, called/N_1156.contig-group-16.g.vcf.gz, called/N_1157.contig-group-16.g.vcf.gz, called/N_1158.contig-group-16.g.vcf.gz, called/N_1344.contig-group-16.g.vcf.gz, called/N_1347.contig-group-16.g.vcf.gz, called/N_1354.contig-group-16.g.vcf.gz, called/N_1355.contig-group-16.g.vcf.gz, called/N_1384.contig-group-16.g.vcf.gz, called/N_1386.contig-group-16.g.vcf.gz, called/N_1390.contig-group-16.g.vcf.gz, called/N_1409.contig-group-16.g.vcf.gz, called/N_1411.contig-group-16.g.vcf.gz, called/N_1413.contig-group-16.g.vcf.gz, called/N_1414.contig-group-16.g.vcf.gz, called/N_1609.contig-group-16.g.vcf.gz, called/N_1870.contig-group-16.g.vcf.gz, called/N_1901.contig-group-16.g.vcf.gz, called/N_1913.contig-group-16.g.vcf.gz, called/N_1927.contig-group-16.g.vcf.gz, called/N_192.contig-group-16.g.vcf.gz, called/N_1934_1_1_368.contig-group-16.g.vcf.gz, called/N_1934_1_1_5973.contig-group-16.g.vcf.gz, called/N_1951_13_1951.contig-group-16.g.vcf.gz, called/N_1992_0123.contig-group-16.g.vcf.gz, called/N_1998_0130.contig-group-16.g.vcf.gz, called/N_2001_0025.contig-group-16.g.vcf.gz, called/N_2001_0205.contig-group-16.g.vcf.gz, called/N_2002_0292.contig-group-16.g.vcf.gz, called/N_2003_5409.contig-group-16.g.vcf.gz, called/N_2004.contig-group-16.g.vcf.gz, called/N_2010_1759.contig-group-16.g.vcf.gz, called/N_21.contig-group-16.g.vcf.gz, called/N_351.contig-group-16.g.vcf.gz, called/N_355.contig-group-16.g.vcf.gz, called/N_401.contig-group-16.g.vcf.gz, called/N_403.contig-group-16.g.vcf.gz, called/N_4843.contig-group-16.g.vcf.gz, called/N_4844.contig-group-16.g.vcf.gz, called/N_4846.contig-group-16.g.vcf.gz, called/N_4847.contig-group-16.g.vcf.gz, called/N_5056.contig-group-16.g.vcf.gz, called/N_5057.contig-group-16.g.vcf.gz, called/N_5129.contig-group-16.g.vcf.gz, called/N_6489.contig-group-16.g.vcf.gz, called/N_6490.contig-group-16.g.vcf.gz, called/N_685.contig-group-16.g.vcf.gz, called/N_689.contig-group-16.g.vcf.gz, called/N_690.contig-group-16.g.vcf.gz, called/N_6926.contig-group-16.g.vcf.gz, called/N_6928.contig-group-16.g.vcf.gz, called/N_6932.contig-group-16.g.vcf.gz, called/N_6.contig-group-16.g.vcf.gz, called/N_7083.contig-group-16.g.vcf.gz, called/N_79.contig-group-16.g.vcf.gz, called/N_7.contig-group-16.g.vcf.gz, called/N_8105.contig-group-16.g.vcf.gz, called/N_8171.contig-group-16.g.vcf.gz, called/N_83.contig-group-16.g.vcf.gz, called/N_8564.contig-group-16.g.vcf.gz, called/N_8565.contig-group-16.g.vcf.gz, called/N_8583.contig-group-16.g.vcf.gz, called/N_8585.contig-group-16.g.vcf.gz, called/N_8586.contig-group-16.g.vcf.gz, called/N_9104.contig-group-16.g.vcf.gz, called/N_9449.contig-group-16.g.vcf.gz, called/N_94.contig-group-16.g.vcf.gz, called/T1481.contig-group-16.g.vcf.gz, called/T1483.contig-group-16.g.vcf.gz, called/T178.contig-group-16.g.vcf.gz, called/T179.contig-group-16.g.vcf.gz, called/T180.contig-group-16.g.vcf.gz, called/T181.contig-group-16.g.vcf.gz, called/T185.contig-group-16.g.vcf.gz, called/T186.contig-group-16.g.vcf.gz, called/T187.contig-group-16.g.vcf.gz, called/T188.contig-group-16.g.vcf.gz, called/T189.contig-group-16.g.vcf.gz, called/T190.contig-group-16.g.vcf.gz, called/T192.contig-group-16.g.vcf.gz, called/T193.contig-group-16.g.vcf.gz, called/T194.contig-group-16.g.vcf.gz, called/T196.contig-group-16.g.vcf.gz, called/T248.contig-group-16.g.vcf.gz, called/T37.contig-group-16.g.vcf.gz, called/T72.contig-group-16.g.vcf.gz, called/T79.contig-group-16.g.vcf.gz, called/M1864_2.contig-group-16.g.vcf.gz.tbi, called/M1865_2.contig-group-16.g.vcf.gz.tbi, called/M5672.contig-group-16.g.vcf.gz.tbi, called/MTDC48361.contig-group-16.g.vcf.gz.tbi, called/N2005.contig-group-16.g.vcf.gz.tbi, called/N_102.contig-group-16.g.vcf.gz.tbi, called/N_1085.contig-group-16.g.vcf.gz.tbi, called/N_1156.contig-group-16.g.vcf.gz.tbi, called/N_1157.contig-group-16.g.vcf.gz.tbi, called/N_1158.contig-group-16.g.vcf.gz.tbi, called/N_1344.contig-group-16.g.vcf.gz.tbi, called/N_1347.contig-group-16.g.vcf.gz.tbi, called/N_1354.contig-group-16.g.vcf.gz.tbi, called/N_1355.contig-group-16.g.vcf.gz.tbi, called/N_1384.contig-group-16.g.vcf.gz.tbi, called/N_1386.contig-group-16.g.vcf.gz.tbi, called/N_1390.contig-group-16.g.vcf.gz.tbi, called/N_1409.contig-group-16.g.vcf.gz.tbi, called/N_1411.contig-group-16.g.vcf.gz.tbi, called/N_1413.contig-group-16.g.vcf.gz.tbi, called/N_1414.contig-group-16.g.vcf.gz.tbi, called/N_1609.contig-group-16.g.vcf.gz.tbi, called/N_1870.contig-group-16.g.vcf.gz.tbi, called/N_1901.contig-group-16.g.vcf.gz.tbi, called/N_1913.contig-group-16.g.vcf.gz.tbi, called/N_1927.contig-group-16.g.vcf.gz.tbi, called/N_192.contig-group-16.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-16.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-16.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-16.g.vcf.gz.tbi, called/N_1992_0123.contig-group-16.g.vcf.gz.tbi, called/N_1998_0130.contig-group-16.g.vcf.gz.tbi, called/N_2001_0025.contig-group-16.g.vcf.gz.tbi, called/N_2001_0205.contig-group-16.g.vcf.gz.tbi, called/N_2002_0292.contig-group-16.g.vcf.gz.tbi, called/N_2003_5409.contig-group-16.g.vcf.gz.tbi, called/N_2004.contig-group-16.g.vcf.gz.tbi, called/N_2010_1759.contig-group-16.g.vcf.gz.tbi, called/N_21.contig-group-16.g.vcf.gz.tbi, called/N_351.contig-group-16.g.vcf.gz.tbi, called/N_355.contig-group-16.g.vcf.gz.tbi, called/N_401.contig-group-16.g.vcf.gz.tbi, called/N_403.contig-group-16.g.vcf.gz.tbi, called/N_4843.contig-group-16.g.vcf.gz.tbi, called/N_4844.contig-group-16.g.vcf.gz.tbi, called/N_4846.contig-group-16.g.vcf.gz.tbi, called/N_4847.contig-group-16.g.vcf.gz.tbi, called/N_5056.contig-group-16.g.vcf.gz.tbi, called/N_5057.contig-group-16.g.vcf.gz.tbi, called/N_5129.contig-group-16.g.vcf.gz.tbi, called/N_6489.contig-group-16.g.vcf.gz.tbi, called/N_6490.contig-group-16.g.vcf.gz.tbi, called/N_685.contig-group-16.g.vcf.gz.tbi, called/N_689.contig-group-16.g.vcf.gz.tbi, called/N_690.contig-group-16.g.vcf.gz.tbi, called/N_6926.contig-group-16.g.vcf.gz.tbi, called/N_6928.contig-group-16.g.vcf.gz.tbi, called/N_6932.contig-group-16.g.vcf.gz.tbi, called/N_6.contig-group-16.g.vcf.gz.tbi, called/N_7083.contig-group-16.g.vcf.gz.tbi, called/N_79.contig-group-16.g.vcf.gz.tbi, called/N_7.contig-group-16.g.vcf.gz.tbi, called/N_8105.contig-group-16.g.vcf.gz.tbi, called/N_8171.contig-group-16.g.vcf.gz.tbi, called/N_83.contig-group-16.g.vcf.gz.tbi, called/N_8564.contig-group-16.g.vcf.gz.tbi, called/N_8565.contig-group-16.g.vcf.gz.tbi, called/N_8583.contig-group-16.g.vcf.gz.tbi, called/N_8585.contig-group-16.g.vcf.gz.tbi, called/N_8586.contig-group-16.g.vcf.gz.tbi, called/N_9104.contig-group-16.g.vcf.gz.tbi, called/N_9449.contig-group-16.g.vcf.gz.tbi, called/N_94.contig-group-16.g.vcf.gz.tbi, called/T1481.contig-group-16.g.vcf.gz.tbi, called/T1483.contig-group-16.g.vcf.gz.tbi, called/T178.contig-group-16.g.vcf.gz.tbi, called/T179.contig-group-16.g.vcf.gz.tbi, called/T180.contig-group-16.g.vcf.gz.tbi, called/T181.contig-group-16.g.vcf.gz.tbi, called/T185.contig-group-16.g.vcf.gz.tbi, called/T186.contig-group-16.g.vcf.gz.tbi, called/T187.contig-group-16.g.vcf.gz.tbi, called/T188.contig-group-16.g.vcf.gz.tbi, called/T189.contig-group-16.g.vcf.gz.tbi, called/T190.contig-group-16.g.vcf.gz.tbi, called/T192.contig-group-16.g.vcf.gz.tbi, called/T193.contig-group-16.g.vcf.gz.tbi, called/T194.contig-group-16.g.vcf.gz.tbi, called/T196.contig-group-16.g.vcf.gz.tbi, called/T248.contig-group-16.g.vcf.gz.tbi, called/T37.contig-group-16.g.vcf.gz.tbi, called/T72.contig-group-16.g.vcf.gz.tbi, called/T79.contig-group-16.g.vcf.gz.tbi output: called/all.contig-group-16.g.vcf.gz, called/all.contig-group-16.g.done log: logs/gatk/combine-gvcfs/contig-group-16.log jobid: 2941 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-16.bench.log reason: Input files updated by another job: called/N_689.contig-group-16.g.vcf.gz, called/N_1158.contig-group-16.g.vcf.gz, called/N_2003_5409.contig-group-16.g.vcf.gz.tbi, called/M5672.contig-group-16.g.vcf.gz, called/N_1157.contig-group-16.g.vcf.gz.tbi, called/N_1927.contig-group-16.g.vcf.gz.tbi, called/N_1927.contig-group-16.g.vcf.gz, called/N_1934_1_1_5973.contig-group-16.g.vcf.gz, called/N_690.contig-group-16.g.vcf.gz, called/N_1158.contig-group-16.g.vcf.gz.tbi, called/N_690.contig-group-16.g.vcf.gz.tbi, called/N_6928.contig-group-16.g.vcf.gz, called/N_1992_0123.contig-group-16.g.vcf.gz, called/N_1609.contig-group-16.g.vcf.gz, called/N_1156.contig-group-16.g.vcf.gz, called/N_5129.contig-group-16.g.vcf.gz, called/T190.contig-group-16.g.vcf.gz, called/N_4847.contig-group-16.g.vcf.gz.tbi, called/N_102.contig-group-16.g.vcf.gz, called/T72.contig-group-16.g.vcf.gz.tbi, called/N_5129.contig-group-16.g.vcf.gz.tbi, called/N_1386.contig-group-16.g.vcf.gz.tbi, called/T72.contig-group-16.g.vcf.gz, called/T187.contig-group-16.g.vcf.gz, called/N2005.contig-group-16.g.vcf.gz, called/N_102.contig-group-16.g.vcf.gz.tbi, called/N_351.contig-group-16.g.vcf.gz, called/N_4847.contig-group-16.g.vcf.gz, called/N_6490.contig-group-16.g.vcf.gz, called/N_9104.contig-group-16.g.vcf.gz, called/N_6489.contig-group-16.g.vcf.gz, called/N_9449.contig-group-16.g.vcf.gz.tbi, called/N_1870.contig-group-16.g.vcf.gz.tbi, called/N_1609.contig-group-16.g.vcf.gz.tbi, called/N_8171.contig-group-16.g.vcf.gz, called/T79.contig-group-16.g.vcf.gz, called/N_1992_0123.contig-group-16.g.vcf.gz.tbi, called/N_83.contig-group-16.g.vcf.gz, called/N_351.contig-group-16.g.vcf.gz.tbi, called/T185.contig-group-16.g.vcf.gz.tbi, called/N2005.contig-group-16.g.vcf.gz.tbi, called/N_689.contig-group-16.g.vcf.gz.tbi, called/N_9104.contig-group-16.g.vcf.gz.tbi, called/N_1386.contig-group-16.g.vcf.gz, called/T187.contig-group-16.g.vcf.gz.tbi, called/T196.contig-group-16.g.vcf.gz, called/N_1354.contig-group-16.g.vcf.gz, called/N_1157.contig-group-16.g.vcf.gz, called/N_4843.contig-group-16.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-16.g.vcf.gz.tbi, called/N_8171.contig-group-16.g.vcf.gz.tbi, called/N_79.contig-group-16.g.vcf.gz.tbi, called/N_8565.contig-group-16.g.vcf.gz, called/T190.contig-group-16.g.vcf.gz.tbi, called/T192.contig-group-16.g.vcf.gz, called/N_2003_5409.contig-group-16.g.vcf.gz, called/N_6489.contig-group-16.g.vcf.gz.tbi, called/T1483.contig-group-16.g.vcf.gz.tbi, called/T185.contig-group-16.g.vcf.gz, called/N_4843.contig-group-16.g.vcf.gz, called/T180.contig-group-16.g.vcf.gz.tbi, called/N_6490.contig-group-16.g.vcf.gz.tbi, called/T192.contig-group-16.g.vcf.gz.tbi, called/N_1354.contig-group-16.g.vcf.gz.tbi, called/T79.contig-group-16.g.vcf.gz.tbi, called/N_83.contig-group-16.g.vcf.gz.tbi, called/N_8583.contig-group-16.g.vcf.gz.tbi, called/T196.contig-group-16.g.vcf.gz.tbi, called/N_79.contig-group-16.g.vcf.gz, called/N_9449.contig-group-16.g.vcf.gz, called/T1483.contig-group-16.g.vcf.gz, called/N_6928.contig-group-16.g.vcf.gz.tbi, called/N_8583.contig-group-16.g.vcf.gz, called/M5672.contig-group-16.g.vcf.gz.tbi, called/N_8565.contig-group-16.g.vcf.gz.tbi, called/T180.contig-group-16.g.vcf.gz, called/N_1870.contig-group-16.g.vcf.gz, called/N_1156.contig-group-16.g.vcf.gz.tbi wildcards: contig=contig-group-16 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-2.g.vcf.gz, called/M1865_2.contig-group-2.g.vcf.gz, called/M5672.contig-group-2.g.vcf.gz, called/MTDC48361.contig-group-2.g.vcf.gz, called/N2005.contig-group-2.g.vcf.gz, called/N_102.contig-group-2.g.vcf.gz, called/N_1085.contig-group-2.g.vcf.gz, called/N_1156.contig-group-2.g.vcf.gz, called/N_1157.contig-group-2.g.vcf.gz, called/N_1158.contig-group-2.g.vcf.gz, called/N_1344.contig-group-2.g.vcf.gz, called/N_1347.contig-group-2.g.vcf.gz, called/N_1354.contig-group-2.g.vcf.gz, called/N_1355.contig-group-2.g.vcf.gz, called/N_1384.contig-group-2.g.vcf.gz, called/N_1386.contig-group-2.g.vcf.gz, called/N_1390.contig-group-2.g.vcf.gz, called/N_1409.contig-group-2.g.vcf.gz, called/N_1411.contig-group-2.g.vcf.gz, called/N_1413.contig-group-2.g.vcf.gz, called/N_1414.contig-group-2.g.vcf.gz, called/N_1609.contig-group-2.g.vcf.gz, called/N_1870.contig-group-2.g.vcf.gz, called/N_1901.contig-group-2.g.vcf.gz, called/N_1913.contig-group-2.g.vcf.gz, called/N_1927.contig-group-2.g.vcf.gz, called/N_192.contig-group-2.g.vcf.gz, called/N_1934_1_1_368.contig-group-2.g.vcf.gz, called/N_1934_1_1_5973.contig-group-2.g.vcf.gz, called/N_1951_13_1951.contig-group-2.g.vcf.gz, called/N_1992_0123.contig-group-2.g.vcf.gz, called/N_1998_0130.contig-group-2.g.vcf.gz, called/N_2001_0025.contig-group-2.g.vcf.gz, called/N_2001_0205.contig-group-2.g.vcf.gz, called/N_2002_0292.contig-group-2.g.vcf.gz, called/N_2003_5409.contig-group-2.g.vcf.gz, called/N_2004.contig-group-2.g.vcf.gz, called/N_2010_1759.contig-group-2.g.vcf.gz, called/N_21.contig-group-2.g.vcf.gz, called/N_351.contig-group-2.g.vcf.gz, called/N_355.contig-group-2.g.vcf.gz, called/N_401.contig-group-2.g.vcf.gz, called/N_403.contig-group-2.g.vcf.gz, called/N_4843.contig-group-2.g.vcf.gz, called/N_4844.contig-group-2.g.vcf.gz, called/N_4846.contig-group-2.g.vcf.gz, called/N_4847.contig-group-2.g.vcf.gz, called/N_5056.contig-group-2.g.vcf.gz, called/N_5057.contig-group-2.g.vcf.gz, called/N_5129.contig-group-2.g.vcf.gz, called/N_6489.contig-group-2.g.vcf.gz, called/N_6490.contig-group-2.g.vcf.gz, called/N_685.contig-group-2.g.vcf.gz, called/N_689.contig-group-2.g.vcf.gz, called/N_690.contig-group-2.g.vcf.gz, called/N_6926.contig-group-2.g.vcf.gz, called/N_6928.contig-group-2.g.vcf.gz, called/N_6932.contig-group-2.g.vcf.gz, called/N_6.contig-group-2.g.vcf.gz, called/N_7083.contig-group-2.g.vcf.gz, called/N_79.contig-group-2.g.vcf.gz, called/N_7.contig-group-2.g.vcf.gz, called/N_8105.contig-group-2.g.vcf.gz, called/N_8171.contig-group-2.g.vcf.gz, called/N_83.contig-group-2.g.vcf.gz, called/N_8564.contig-group-2.g.vcf.gz, called/N_8565.contig-group-2.g.vcf.gz, called/N_8583.contig-group-2.g.vcf.gz, called/N_8585.contig-group-2.g.vcf.gz, called/N_8586.contig-group-2.g.vcf.gz, called/N_9104.contig-group-2.g.vcf.gz, called/N_9449.contig-group-2.g.vcf.gz, called/N_94.contig-group-2.g.vcf.gz, called/T1481.contig-group-2.g.vcf.gz, called/T1483.contig-group-2.g.vcf.gz, called/T178.contig-group-2.g.vcf.gz, called/T179.contig-group-2.g.vcf.gz, called/T180.contig-group-2.g.vcf.gz, called/T181.contig-group-2.g.vcf.gz, called/T185.contig-group-2.g.vcf.gz, called/T186.contig-group-2.g.vcf.gz, called/T187.contig-group-2.g.vcf.gz, called/T188.contig-group-2.g.vcf.gz, called/T189.contig-group-2.g.vcf.gz, called/T190.contig-group-2.g.vcf.gz, called/T192.contig-group-2.g.vcf.gz, called/T193.contig-group-2.g.vcf.gz, called/T194.contig-group-2.g.vcf.gz, called/T196.contig-group-2.g.vcf.gz, called/T248.contig-group-2.g.vcf.gz, called/T37.contig-group-2.g.vcf.gz, called/T72.contig-group-2.g.vcf.gz, called/T79.contig-group-2.g.vcf.gz, called/M1864_2.contig-group-2.g.vcf.gz.tbi, called/M1865_2.contig-group-2.g.vcf.gz.tbi, called/M5672.contig-group-2.g.vcf.gz.tbi, called/MTDC48361.contig-group-2.g.vcf.gz.tbi, called/N2005.contig-group-2.g.vcf.gz.tbi, called/N_102.contig-group-2.g.vcf.gz.tbi, called/N_1085.contig-group-2.g.vcf.gz.tbi, called/N_1156.contig-group-2.g.vcf.gz.tbi, called/N_1157.contig-group-2.g.vcf.gz.tbi, called/N_1158.contig-group-2.g.vcf.gz.tbi, called/N_1344.contig-group-2.g.vcf.gz.tbi, called/N_1347.contig-group-2.g.vcf.gz.tbi, called/N_1354.contig-group-2.g.vcf.gz.tbi, called/N_1355.contig-group-2.g.vcf.gz.tbi, called/N_1384.contig-group-2.g.vcf.gz.tbi, called/N_1386.contig-group-2.g.vcf.gz.tbi, called/N_1390.contig-group-2.g.vcf.gz.tbi, called/N_1409.contig-group-2.g.vcf.gz.tbi, called/N_1411.contig-group-2.g.vcf.gz.tbi, called/N_1413.contig-group-2.g.vcf.gz.tbi, called/N_1414.contig-group-2.g.vcf.gz.tbi, called/N_1609.contig-group-2.g.vcf.gz.tbi, called/N_1870.contig-group-2.g.vcf.gz.tbi, called/N_1901.contig-group-2.g.vcf.gz.tbi, called/N_1913.contig-group-2.g.vcf.gz.tbi, called/N_1927.contig-group-2.g.vcf.gz.tbi, called/N_192.contig-group-2.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-2.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-2.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-2.g.vcf.gz.tbi, called/N_1992_0123.contig-group-2.g.vcf.gz.tbi, called/N_1998_0130.contig-group-2.g.vcf.gz.tbi, called/N_2001_0025.contig-group-2.g.vcf.gz.tbi, called/N_2001_0205.contig-group-2.g.vcf.gz.tbi, called/N_2002_0292.contig-group-2.g.vcf.gz.tbi, called/N_2003_5409.contig-group-2.g.vcf.gz.tbi, called/N_2004.contig-group-2.g.vcf.gz.tbi, called/N_2010_1759.contig-group-2.g.vcf.gz.tbi, called/N_21.contig-group-2.g.vcf.gz.tbi, called/N_351.contig-group-2.g.vcf.gz.tbi, called/N_355.contig-group-2.g.vcf.gz.tbi, called/N_401.contig-group-2.g.vcf.gz.tbi, called/N_403.contig-group-2.g.vcf.gz.tbi, called/N_4843.contig-group-2.g.vcf.gz.tbi, called/N_4844.contig-group-2.g.vcf.gz.tbi, called/N_4846.contig-group-2.g.vcf.gz.tbi, called/N_4847.contig-group-2.g.vcf.gz.tbi, called/N_5056.contig-group-2.g.vcf.gz.tbi, called/N_5057.contig-group-2.g.vcf.gz.tbi, called/N_5129.contig-group-2.g.vcf.gz.tbi, called/N_6489.contig-group-2.g.vcf.gz.tbi, called/N_6490.contig-group-2.g.vcf.gz.tbi, called/N_685.contig-group-2.g.vcf.gz.tbi, called/N_689.contig-group-2.g.vcf.gz.tbi, called/N_690.contig-group-2.g.vcf.gz.tbi, called/N_6926.contig-group-2.g.vcf.gz.tbi, called/N_6928.contig-group-2.g.vcf.gz.tbi, called/N_6932.contig-group-2.g.vcf.gz.tbi, called/N_6.contig-group-2.g.vcf.gz.tbi, called/N_7083.contig-group-2.g.vcf.gz.tbi, called/N_79.contig-group-2.g.vcf.gz.tbi, called/N_7.contig-group-2.g.vcf.gz.tbi, called/N_8105.contig-group-2.g.vcf.gz.tbi, called/N_8171.contig-group-2.g.vcf.gz.tbi, called/N_83.contig-group-2.g.vcf.gz.tbi, called/N_8564.contig-group-2.g.vcf.gz.tbi, called/N_8565.contig-group-2.g.vcf.gz.tbi, called/N_8583.contig-group-2.g.vcf.gz.tbi, called/N_8585.contig-group-2.g.vcf.gz.tbi, called/N_8586.contig-group-2.g.vcf.gz.tbi, called/N_9104.contig-group-2.g.vcf.gz.tbi, called/N_9449.contig-group-2.g.vcf.gz.tbi, called/N_94.contig-group-2.g.vcf.gz.tbi, called/T1481.contig-group-2.g.vcf.gz.tbi, called/T1483.contig-group-2.g.vcf.gz.tbi, called/T178.contig-group-2.g.vcf.gz.tbi, called/T179.contig-group-2.g.vcf.gz.tbi, called/T180.contig-group-2.g.vcf.gz.tbi, called/T181.contig-group-2.g.vcf.gz.tbi, called/T185.contig-group-2.g.vcf.gz.tbi, called/T186.contig-group-2.g.vcf.gz.tbi, called/T187.contig-group-2.g.vcf.gz.tbi, called/T188.contig-group-2.g.vcf.gz.tbi, called/T189.contig-group-2.g.vcf.gz.tbi, called/T190.contig-group-2.g.vcf.gz.tbi, called/T192.contig-group-2.g.vcf.gz.tbi, called/T193.contig-group-2.g.vcf.gz.tbi, called/T194.contig-group-2.g.vcf.gz.tbi, called/T196.contig-group-2.g.vcf.gz.tbi, called/T248.contig-group-2.g.vcf.gz.tbi, called/T37.contig-group-2.g.vcf.gz.tbi, called/T72.contig-group-2.g.vcf.gz.tbi, called/T79.contig-group-2.g.vcf.gz.tbi output: called/all.contig-group-2.g.vcf.gz, called/all.contig-group-2.g.done log: logs/gatk/combine-gvcfs/contig-group-2.log jobid: 1597 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-2.bench.log reason: Missing output files: called/all.contig-group-2.g.vcf.gz; Input files updated by another job: called/N_83.contig-group-2.g.vcf.gz.tbi, called/T190.contig-group-2.g.vcf.gz, called/N_351.contig-group-2.g.vcf.gz, called/M5672.contig-group-2.g.vcf.gz.tbi, called/T187.contig-group-2.g.vcf.gz.tbi, called/T192.contig-group-2.g.vcf.gz, called/N_689.contig-group-2.g.vcf.gz.tbi, called/N_1927.contig-group-2.g.vcf.gz.tbi, called/T79.contig-group-2.g.vcf.gz, called/N_79.contig-group-2.g.vcf.gz.tbi, called/N_79.contig-group-2.g.vcf.gz, called/N2005.contig-group-2.g.vcf.gz.tbi, called/N_6928.contig-group-2.g.vcf.gz, called/T180.contig-group-2.g.vcf.gz, called/N_2002_0292.contig-group-2.g.vcf.gz.tbi, called/N_1354.contig-group-2.g.vcf.gz.tbi, called/N_4847.contig-group-2.g.vcf.gz, called/N_4843.contig-group-2.g.vcf.gz, called/N_1156.contig-group-2.g.vcf.gz.tbi, called/N_1992_0123.contig-group-2.g.vcf.gz.tbi, called/T187.contig-group-2.g.vcf.gz, called/N_1609.contig-group-2.g.vcf.gz.tbi, called/T185.contig-group-2.g.vcf.gz, called/N_1992_0123.contig-group-2.g.vcf.gz, called/N_8171.contig-group-2.g.vcf.gz, called/N_1927.contig-group-2.g.vcf.gz, called/N_1386.contig-group-2.g.vcf.gz.tbi, called/N_9104.contig-group-2.g.vcf.gz, called/T180.contig-group-2.g.vcf.gz.tbi, called/N_689.contig-group-2.g.vcf.gz, called/N_6489.contig-group-2.g.vcf.gz.tbi, called/N_9449.contig-group-2.g.vcf.gz.tbi, called/N_2003_5409.contig-group-2.g.vcf.gz, called/N_6490.contig-group-2.g.vcf.gz.tbi, called/N_8565.contig-group-2.g.vcf.gz, called/N_8171.contig-group-2.g.vcf.gz.tbi, called/N_4847.contig-group-2.g.vcf.gz.tbi, called/N_1157.contig-group-2.g.vcf.gz, called/T1483.contig-group-2.g.vcf.gz.tbi, called/N_690.contig-group-2.g.vcf.gz.tbi, called/N_8583.contig-group-2.g.vcf.gz.tbi, called/N_2002_0292.contig-group-2.g.vcf.gz, called/N_5129.contig-group-2.g.vcf.gz, called/N_8565.contig-group-2.g.vcf.gz.tbi, called/N_102.contig-group-2.g.vcf.gz, called/T79.contig-group-2.g.vcf.gz.tbi, called/N_5129.contig-group-2.g.vcf.gz.tbi, called/N_6489.contig-group-2.g.vcf.gz, called/N_8583.contig-group-2.g.vcf.gz, called/N_2003_5409.contig-group-2.g.vcf.gz.tbi, called/M5672.contig-group-2.g.vcf.gz, called/N_1354.contig-group-2.g.vcf.gz, called/T185.contig-group-2.g.vcf.gz.tbi, called/N_1386.contig-group-2.g.vcf.gz, called/N2005.contig-group-2.g.vcf.gz, called/N_102.contig-group-2.g.vcf.gz.tbi, called/N_690.contig-group-2.g.vcf.gz, called/N_6928.contig-group-2.g.vcf.gz.tbi, called/N_1870.contig-group-2.g.vcf.gz, called/N_83.contig-group-2.g.vcf.gz, called/N_1157.contig-group-2.g.vcf.gz.tbi, called/T72.contig-group-2.g.vcf.gz.tbi, called/N_1156.contig-group-2.g.vcf.gz, called/N_9104.contig-group-2.g.vcf.gz.tbi, called/T192.contig-group-2.g.vcf.gz.tbi, called/N_351.contig-group-2.g.vcf.gz.tbi, called/T190.contig-group-2.g.vcf.gz.tbi, called/T196.contig-group-2.g.vcf.gz, called/N_1158.contig-group-2.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-2.g.vcf.gz.tbi, called/N_1870.contig-group-2.g.vcf.gz.tbi, called/N_4843.contig-group-2.g.vcf.gz.tbi, called/T196.contig-group-2.g.vcf.gz.tbi, called/N_1158.contig-group-2.g.vcf.gz, called/T1483.contig-group-2.g.vcf.gz, called/N_1934_1_1_5973.contig-group-2.g.vcf.gz, called/N_6490.contig-group-2.g.vcf.gz, called/N_9449.contig-group-2.g.vcf.gz, called/N_1609.contig-group-2.g.vcf.gz, called/T72.contig-group-2.g.vcf.gz wildcards: contig=contig-group-2 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-23.g.vcf.gz, called/M1865_2.contig-group-23.g.vcf.gz, called/M5672.contig-group-23.g.vcf.gz, called/MTDC48361.contig-group-23.g.vcf.gz, called/N2005.contig-group-23.g.vcf.gz, called/N_102.contig-group-23.g.vcf.gz, called/N_1085.contig-group-23.g.vcf.gz, called/N_1156.contig-group-23.g.vcf.gz, called/N_1157.contig-group-23.g.vcf.gz, called/N_1158.contig-group-23.g.vcf.gz, called/N_1344.contig-group-23.g.vcf.gz, called/N_1347.contig-group-23.g.vcf.gz, called/N_1354.contig-group-23.g.vcf.gz, called/N_1355.contig-group-23.g.vcf.gz, called/N_1384.contig-group-23.g.vcf.gz, called/N_1386.contig-group-23.g.vcf.gz, called/N_1390.contig-group-23.g.vcf.gz, called/N_1409.contig-group-23.g.vcf.gz, called/N_1411.contig-group-23.g.vcf.gz, called/N_1413.contig-group-23.g.vcf.gz, called/N_1414.contig-group-23.g.vcf.gz, called/N_1609.contig-group-23.g.vcf.gz, called/N_1870.contig-group-23.g.vcf.gz, called/N_1901.contig-group-23.g.vcf.gz, called/N_1913.contig-group-23.g.vcf.gz, called/N_1927.contig-group-23.g.vcf.gz, called/N_192.contig-group-23.g.vcf.gz, called/N_1934_1_1_368.contig-group-23.g.vcf.gz, called/N_1934_1_1_5973.contig-group-23.g.vcf.gz, called/N_1951_13_1951.contig-group-23.g.vcf.gz, called/N_1992_0123.contig-group-23.g.vcf.gz, called/N_1998_0130.contig-group-23.g.vcf.gz, called/N_2001_0025.contig-group-23.g.vcf.gz, called/N_2001_0205.contig-group-23.g.vcf.gz, called/N_2002_0292.contig-group-23.g.vcf.gz, called/N_2003_5409.contig-group-23.g.vcf.gz, called/N_2004.contig-group-23.g.vcf.gz, called/N_2010_1759.contig-group-23.g.vcf.gz, called/N_21.contig-group-23.g.vcf.gz, called/N_351.contig-group-23.g.vcf.gz, called/N_355.contig-group-23.g.vcf.gz, called/N_401.contig-group-23.g.vcf.gz, called/N_403.contig-group-23.g.vcf.gz, called/N_4843.contig-group-23.g.vcf.gz, called/N_4844.contig-group-23.g.vcf.gz, called/N_4846.contig-group-23.g.vcf.gz, called/N_4847.contig-group-23.g.vcf.gz, called/N_5056.contig-group-23.g.vcf.gz, called/N_5057.contig-group-23.g.vcf.gz, called/N_5129.contig-group-23.g.vcf.gz, called/N_6489.contig-group-23.g.vcf.gz, called/N_6490.contig-group-23.g.vcf.gz, called/N_685.contig-group-23.g.vcf.gz, called/N_689.contig-group-23.g.vcf.gz, called/N_690.contig-group-23.g.vcf.gz, called/N_6926.contig-group-23.g.vcf.gz, called/N_6928.contig-group-23.g.vcf.gz, called/N_6932.contig-group-23.g.vcf.gz, called/N_6.contig-group-23.g.vcf.gz, called/N_7083.contig-group-23.g.vcf.gz, called/N_79.contig-group-23.g.vcf.gz, called/N_7.contig-group-23.g.vcf.gz, called/N_8105.contig-group-23.g.vcf.gz, called/N_8171.contig-group-23.g.vcf.gz, called/N_83.contig-group-23.g.vcf.gz, called/N_8564.contig-group-23.g.vcf.gz, called/N_8565.contig-group-23.g.vcf.gz, called/N_8583.contig-group-23.g.vcf.gz, called/N_8585.contig-group-23.g.vcf.gz, called/N_8586.contig-group-23.g.vcf.gz, called/N_9104.contig-group-23.g.vcf.gz, called/N_9449.contig-group-23.g.vcf.gz, called/N_94.contig-group-23.g.vcf.gz, called/T1481.contig-group-23.g.vcf.gz, called/T1483.contig-group-23.g.vcf.gz, called/T178.contig-group-23.g.vcf.gz, called/T179.contig-group-23.g.vcf.gz, called/T180.contig-group-23.g.vcf.gz, called/T181.contig-group-23.g.vcf.gz, called/T185.contig-group-23.g.vcf.gz, called/T186.contig-group-23.g.vcf.gz, called/T187.contig-group-23.g.vcf.gz, called/T188.contig-group-23.g.vcf.gz, called/T189.contig-group-23.g.vcf.gz, called/T190.contig-group-23.g.vcf.gz, called/T192.contig-group-23.g.vcf.gz, called/T193.contig-group-23.g.vcf.gz, called/T194.contig-group-23.g.vcf.gz, called/T196.contig-group-23.g.vcf.gz, called/T248.contig-group-23.g.vcf.gz, called/T37.contig-group-23.g.vcf.gz, called/T72.contig-group-23.g.vcf.gz, called/T79.contig-group-23.g.vcf.gz, called/M1864_2.contig-group-23.g.vcf.gz.tbi, called/M1865_2.contig-group-23.g.vcf.gz.tbi, called/M5672.contig-group-23.g.vcf.gz.tbi, called/MTDC48361.contig-group-23.g.vcf.gz.tbi, called/N2005.contig-group-23.g.vcf.gz.tbi, called/N_102.contig-group-23.g.vcf.gz.tbi, called/N_1085.contig-group-23.g.vcf.gz.tbi, called/N_1156.contig-group-23.g.vcf.gz.tbi, called/N_1157.contig-group-23.g.vcf.gz.tbi, called/N_1158.contig-group-23.g.vcf.gz.tbi, called/N_1344.contig-group-23.g.vcf.gz.tbi, called/N_1347.contig-group-23.g.vcf.gz.tbi, called/N_1354.contig-group-23.g.vcf.gz.tbi, called/N_1355.contig-group-23.g.vcf.gz.tbi, called/N_1384.contig-group-23.g.vcf.gz.tbi, called/N_1386.contig-group-23.g.vcf.gz.tbi, called/N_1390.contig-group-23.g.vcf.gz.tbi, called/N_1409.contig-group-23.g.vcf.gz.tbi, called/N_1411.contig-group-23.g.vcf.gz.tbi, called/N_1413.contig-group-23.g.vcf.gz.tbi, called/N_1414.contig-group-23.g.vcf.gz.tbi, called/N_1609.contig-group-23.g.vcf.gz.tbi, called/N_1870.contig-group-23.g.vcf.gz.tbi, called/N_1901.contig-group-23.g.vcf.gz.tbi, called/N_1913.contig-group-23.g.vcf.gz.tbi, called/N_1927.contig-group-23.g.vcf.gz.tbi, called/N_192.contig-group-23.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-23.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-23.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-23.g.vcf.gz.tbi, called/N_1992_0123.contig-group-23.g.vcf.gz.tbi, called/N_1998_0130.contig-group-23.g.vcf.gz.tbi, called/N_2001_0025.contig-group-23.g.vcf.gz.tbi, called/N_2001_0205.contig-group-23.g.vcf.gz.tbi, called/N_2002_0292.contig-group-23.g.vcf.gz.tbi, called/N_2003_5409.contig-group-23.g.vcf.gz.tbi, called/N_2004.contig-group-23.g.vcf.gz.tbi, called/N_2010_1759.contig-group-23.g.vcf.gz.tbi, called/N_21.contig-group-23.g.vcf.gz.tbi, called/N_351.contig-group-23.g.vcf.gz.tbi, called/N_355.contig-group-23.g.vcf.gz.tbi, called/N_401.contig-group-23.g.vcf.gz.tbi, called/N_403.contig-group-23.g.vcf.gz.tbi, called/N_4843.contig-group-23.g.vcf.gz.tbi, called/N_4844.contig-group-23.g.vcf.gz.tbi, called/N_4846.contig-group-23.g.vcf.gz.tbi, called/N_4847.contig-group-23.g.vcf.gz.tbi, called/N_5056.contig-group-23.g.vcf.gz.tbi, called/N_5057.contig-group-23.g.vcf.gz.tbi, called/N_5129.contig-group-23.g.vcf.gz.tbi, called/N_6489.contig-group-23.g.vcf.gz.tbi, called/N_6490.contig-group-23.g.vcf.gz.tbi, called/N_685.contig-group-23.g.vcf.gz.tbi, called/N_689.contig-group-23.g.vcf.gz.tbi, called/N_690.contig-group-23.g.vcf.gz.tbi, called/N_6926.contig-group-23.g.vcf.gz.tbi, called/N_6928.contig-group-23.g.vcf.gz.tbi, called/N_6932.contig-group-23.g.vcf.gz.tbi, called/N_6.contig-group-23.g.vcf.gz.tbi, called/N_7083.contig-group-23.g.vcf.gz.tbi, called/N_79.contig-group-23.g.vcf.gz.tbi, called/N_7.contig-group-23.g.vcf.gz.tbi, called/N_8105.contig-group-23.g.vcf.gz.tbi, called/N_8171.contig-group-23.g.vcf.gz.tbi, called/N_83.contig-group-23.g.vcf.gz.tbi, called/N_8564.contig-group-23.g.vcf.gz.tbi, called/N_8565.contig-group-23.g.vcf.gz.tbi, called/N_8583.contig-group-23.g.vcf.gz.tbi, called/N_8585.contig-group-23.g.vcf.gz.tbi, called/N_8586.contig-group-23.g.vcf.gz.tbi, called/N_9104.contig-group-23.g.vcf.gz.tbi, called/N_9449.contig-group-23.g.vcf.gz.tbi, called/N_94.contig-group-23.g.vcf.gz.tbi, called/T1481.contig-group-23.g.vcf.gz.tbi, called/T1483.contig-group-23.g.vcf.gz.tbi, called/T178.contig-group-23.g.vcf.gz.tbi, called/T179.contig-group-23.g.vcf.gz.tbi, called/T180.contig-group-23.g.vcf.gz.tbi, called/T181.contig-group-23.g.vcf.gz.tbi, called/T185.contig-group-23.g.vcf.gz.tbi, called/T186.contig-group-23.g.vcf.gz.tbi, called/T187.contig-group-23.g.vcf.gz.tbi, called/T188.contig-group-23.g.vcf.gz.tbi, called/T189.contig-group-23.g.vcf.gz.tbi, called/T190.contig-group-23.g.vcf.gz.tbi, called/T192.contig-group-23.g.vcf.gz.tbi, called/T193.contig-group-23.g.vcf.gz.tbi, called/T194.contig-group-23.g.vcf.gz.tbi, called/T196.contig-group-23.g.vcf.gz.tbi, called/T248.contig-group-23.g.vcf.gz.tbi, called/T37.contig-group-23.g.vcf.gz.tbi, called/T72.contig-group-23.g.vcf.gz.tbi, called/T79.contig-group-23.g.vcf.gz.tbi output: called/all.contig-group-23.g.vcf.gz, called/all.contig-group-23.g.done log: logs/gatk/combine-gvcfs/contig-group-23.log jobid: 3613 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-23.bench.log reason: Input files updated by another job: called/T180.contig-group-23.g.vcf.gz, called/M5672.contig-group-23.g.vcf.gz, called/N_1386.contig-group-23.g.vcf.gz.tbi, called/N_4843.contig-group-23.g.vcf.gz.tbi, called/N_1927.contig-group-23.g.vcf.gz, called/N_83.contig-group-23.g.vcf.gz.tbi, called/N_1609.contig-group-23.g.vcf.gz.tbi, called/N_8171.contig-group-23.g.vcf.gz.tbi, called/N_1609.contig-group-23.g.vcf.gz, called/T196.contig-group-23.g.vcf.gz.tbi, called/N_689.contig-group-23.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-23.g.vcf.gz.tbi, called/N_1156.contig-group-23.g.vcf.gz.tbi, called/N_6928.contig-group-23.g.vcf.gz, called/N_1870.contig-group-23.g.vcf.gz.tbi, called/T180.contig-group-23.g.vcf.gz.tbi, called/N_1158.contig-group-23.g.vcf.gz, called/N_1354.contig-group-23.g.vcf.gz, called/T196.contig-group-23.g.vcf.gz, called/T72.contig-group-23.g.vcf.gz, called/T190.contig-group-23.g.vcf.gz, called/N_2003_5409.contig-group-23.g.vcf.gz, called/N_83.contig-group-23.g.vcf.gz, called/N_1992_0123.contig-group-23.g.vcf.gz, called/N_1992_0123.contig-group-23.g.vcf.gz.tbi, called/N_4843.contig-group-23.g.vcf.gz, called/N_102.contig-group-23.g.vcf.gz.tbi, called/N_8171.contig-group-23.g.vcf.gz, called/T185.contig-group-23.g.vcf.gz, called/N_9104.contig-group-23.g.vcf.gz.tbi, called/N_1927.contig-group-23.g.vcf.gz.tbi, called/T185.contig-group-23.g.vcf.gz.tbi, called/N_690.contig-group-23.g.vcf.gz, called/N_102.contig-group-23.g.vcf.gz, called/N_1354.contig-group-23.g.vcf.gz.tbi, called/N_351.contig-group-23.g.vcf.gz, called/N_8583.contig-group-23.g.vcf.gz, called/N_6490.contig-group-23.g.vcf.gz, called/N_6489.contig-group-23.g.vcf.gz, called/N_1386.contig-group-23.g.vcf.gz, called/N_8565.contig-group-23.g.vcf.gz.tbi, called/N2005.contig-group-23.g.vcf.gz.tbi, called/N_1158.contig-group-23.g.vcf.gz.tbi, called/T1483.contig-group-23.g.vcf.gz, called/N_6490.contig-group-23.g.vcf.gz.tbi, called/T187.contig-group-23.g.vcf.gz.tbi, called/N_2003_5409.contig-group-23.g.vcf.gz.tbi, called/N_8565.contig-group-23.g.vcf.gz, called/N_4847.contig-group-23.g.vcf.gz.tbi, called/N_1157.contig-group-23.g.vcf.gz, called/N_1870.contig-group-23.g.vcf.gz, called/N_79.contig-group-23.g.vcf.gz, called/N_689.contig-group-23.g.vcf.gz, called/N_1156.contig-group-23.g.vcf.gz, called/N_1934_1_1_5973.contig-group-23.g.vcf.gz, called/N_690.contig-group-23.g.vcf.gz.tbi, called/M5672.contig-group-23.g.vcf.gz.tbi, called/N_9104.contig-group-23.g.vcf.gz, called/T192.contig-group-23.g.vcf.gz.tbi, called/N_6489.contig-group-23.g.vcf.gz.tbi, called/N_6928.contig-group-23.g.vcf.gz.tbi, called/T187.contig-group-23.g.vcf.gz, called/T192.contig-group-23.g.vcf.gz, called/N_79.contig-group-23.g.vcf.gz.tbi, called/T1483.contig-group-23.g.vcf.gz.tbi, called/T79.contig-group-23.g.vcf.gz.tbi, called/N_9449.contig-group-23.g.vcf.gz.tbi, called/T79.contig-group-23.g.vcf.gz, called/N_4847.contig-group-23.g.vcf.gz, called/N_351.contig-group-23.g.vcf.gz.tbi, called/N_1157.contig-group-23.g.vcf.gz.tbi, called/N_9449.contig-group-23.g.vcf.gz, called/T190.contig-group-23.g.vcf.gz.tbi, called/N2005.contig-group-23.g.vcf.gz, called/N_8583.contig-group-23.g.vcf.gz.tbi, called/T72.contig-group-23.g.vcf.gz.tbi, called/N_5129.contig-group-23.g.vcf.gz, called/N_5129.contig-group-23.g.vcf.gz.tbi wildcards: contig=contig-group-23 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-9.g.vcf.gz, called/M1865_2.contig-group-9.g.vcf.gz, called/M5672.contig-group-9.g.vcf.gz, called/MTDC48361.contig-group-9.g.vcf.gz, called/N2005.contig-group-9.g.vcf.gz, called/N_102.contig-group-9.g.vcf.gz, called/N_1085.contig-group-9.g.vcf.gz, called/N_1156.contig-group-9.g.vcf.gz, called/N_1157.contig-group-9.g.vcf.gz, called/N_1158.contig-group-9.g.vcf.gz, called/N_1344.contig-group-9.g.vcf.gz, called/N_1347.contig-group-9.g.vcf.gz, called/N_1354.contig-group-9.g.vcf.gz, called/N_1355.contig-group-9.g.vcf.gz, called/N_1384.contig-group-9.g.vcf.gz, called/N_1386.contig-group-9.g.vcf.gz, called/N_1390.contig-group-9.g.vcf.gz, called/N_1409.contig-group-9.g.vcf.gz, called/N_1411.contig-group-9.g.vcf.gz, called/N_1413.contig-group-9.g.vcf.gz, called/N_1414.contig-group-9.g.vcf.gz, called/N_1609.contig-group-9.g.vcf.gz, called/N_1870.contig-group-9.g.vcf.gz, called/N_1901.contig-group-9.g.vcf.gz, called/N_1913.contig-group-9.g.vcf.gz, called/N_1927.contig-group-9.g.vcf.gz, called/N_192.contig-group-9.g.vcf.gz, called/N_1934_1_1_368.contig-group-9.g.vcf.gz, called/N_1934_1_1_5973.contig-group-9.g.vcf.gz, called/N_1951_13_1951.contig-group-9.g.vcf.gz, called/N_1992_0123.contig-group-9.g.vcf.gz, called/N_1998_0130.contig-group-9.g.vcf.gz, called/N_2001_0025.contig-group-9.g.vcf.gz, called/N_2001_0205.contig-group-9.g.vcf.gz, called/N_2002_0292.contig-group-9.g.vcf.gz, called/N_2003_5409.contig-group-9.g.vcf.gz, called/N_2004.contig-group-9.g.vcf.gz, called/N_2010_1759.contig-group-9.g.vcf.gz, called/N_21.contig-group-9.g.vcf.gz, called/N_351.contig-group-9.g.vcf.gz, called/N_355.contig-group-9.g.vcf.gz, called/N_401.contig-group-9.g.vcf.gz, called/N_403.contig-group-9.g.vcf.gz, called/N_4843.contig-group-9.g.vcf.gz, called/N_4844.contig-group-9.g.vcf.gz, called/N_4846.contig-group-9.g.vcf.gz, called/N_4847.contig-group-9.g.vcf.gz, called/N_5056.contig-group-9.g.vcf.gz, called/N_5057.contig-group-9.g.vcf.gz, called/N_5129.contig-group-9.g.vcf.gz, called/N_6489.contig-group-9.g.vcf.gz, called/N_6490.contig-group-9.g.vcf.gz, called/N_685.contig-group-9.g.vcf.gz, called/N_689.contig-group-9.g.vcf.gz, called/N_690.contig-group-9.g.vcf.gz, called/N_6926.contig-group-9.g.vcf.gz, called/N_6928.contig-group-9.g.vcf.gz, called/N_6932.contig-group-9.g.vcf.gz, called/N_6.contig-group-9.g.vcf.gz, called/N_7083.contig-group-9.g.vcf.gz, called/N_79.contig-group-9.g.vcf.gz, called/N_7.contig-group-9.g.vcf.gz, called/N_8105.contig-group-9.g.vcf.gz, called/N_8171.contig-group-9.g.vcf.gz, called/N_83.contig-group-9.g.vcf.gz, called/N_8564.contig-group-9.g.vcf.gz, called/N_8565.contig-group-9.g.vcf.gz, called/N_8583.contig-group-9.g.vcf.gz, called/N_8585.contig-group-9.g.vcf.gz, called/N_8586.contig-group-9.g.vcf.gz, called/N_9104.contig-group-9.g.vcf.gz, called/N_9449.contig-group-9.g.vcf.gz, called/N_94.contig-group-9.g.vcf.gz, called/T1481.contig-group-9.g.vcf.gz, called/T1483.contig-group-9.g.vcf.gz, called/T178.contig-group-9.g.vcf.gz, called/T179.contig-group-9.g.vcf.gz, called/T180.contig-group-9.g.vcf.gz, called/T181.contig-group-9.g.vcf.gz, called/T185.contig-group-9.g.vcf.gz, called/T186.contig-group-9.g.vcf.gz, called/T187.contig-group-9.g.vcf.gz, called/T188.contig-group-9.g.vcf.gz, called/T189.contig-group-9.g.vcf.gz, called/T190.contig-group-9.g.vcf.gz, called/T192.contig-group-9.g.vcf.gz, called/T193.contig-group-9.g.vcf.gz, called/T194.contig-group-9.g.vcf.gz, called/T196.contig-group-9.g.vcf.gz, called/T248.contig-group-9.g.vcf.gz, called/T37.contig-group-9.g.vcf.gz, called/T72.contig-group-9.g.vcf.gz, called/T79.contig-group-9.g.vcf.gz, called/M1864_2.contig-group-9.g.vcf.gz.tbi, called/M1865_2.contig-group-9.g.vcf.gz.tbi, called/M5672.contig-group-9.g.vcf.gz.tbi, called/MTDC48361.contig-group-9.g.vcf.gz.tbi, called/N2005.contig-group-9.g.vcf.gz.tbi, called/N_102.contig-group-9.g.vcf.gz.tbi, called/N_1085.contig-group-9.g.vcf.gz.tbi, called/N_1156.contig-group-9.g.vcf.gz.tbi, called/N_1157.contig-group-9.g.vcf.gz.tbi, called/N_1158.contig-group-9.g.vcf.gz.tbi, called/N_1344.contig-group-9.g.vcf.gz.tbi, called/N_1347.contig-group-9.g.vcf.gz.tbi, called/N_1354.contig-group-9.g.vcf.gz.tbi, called/N_1355.contig-group-9.g.vcf.gz.tbi, called/N_1384.contig-group-9.g.vcf.gz.tbi, called/N_1386.contig-group-9.g.vcf.gz.tbi, called/N_1390.contig-group-9.g.vcf.gz.tbi, called/N_1409.contig-group-9.g.vcf.gz.tbi, called/N_1411.contig-group-9.g.vcf.gz.tbi, called/N_1413.contig-group-9.g.vcf.gz.tbi, called/N_1414.contig-group-9.g.vcf.gz.tbi, called/N_1609.contig-group-9.g.vcf.gz.tbi, called/N_1870.contig-group-9.g.vcf.gz.tbi, called/N_1901.contig-group-9.g.vcf.gz.tbi, called/N_1913.contig-group-9.g.vcf.gz.tbi, called/N_1927.contig-group-9.g.vcf.gz.tbi, called/N_192.contig-group-9.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-9.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-9.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-9.g.vcf.gz.tbi, called/N_1992_0123.contig-group-9.g.vcf.gz.tbi, called/N_1998_0130.contig-group-9.g.vcf.gz.tbi, called/N_2001_0025.contig-group-9.g.vcf.gz.tbi, called/N_2001_0205.contig-group-9.g.vcf.gz.tbi, called/N_2002_0292.contig-group-9.g.vcf.gz.tbi, called/N_2003_5409.contig-group-9.g.vcf.gz.tbi, called/N_2004.contig-group-9.g.vcf.gz.tbi, called/N_2010_1759.contig-group-9.g.vcf.gz.tbi, called/N_21.contig-group-9.g.vcf.gz.tbi, called/N_351.contig-group-9.g.vcf.gz.tbi, called/N_355.contig-group-9.g.vcf.gz.tbi, called/N_401.contig-group-9.g.vcf.gz.tbi, called/N_403.contig-group-9.g.vcf.gz.tbi, called/N_4843.contig-group-9.g.vcf.gz.tbi, called/N_4844.contig-group-9.g.vcf.gz.tbi, called/N_4846.contig-group-9.g.vcf.gz.tbi, called/N_4847.contig-group-9.g.vcf.gz.tbi, called/N_5056.contig-group-9.g.vcf.gz.tbi, called/N_5057.contig-group-9.g.vcf.gz.tbi, called/N_5129.contig-group-9.g.vcf.gz.tbi, called/N_6489.contig-group-9.g.vcf.gz.tbi, called/N_6490.contig-group-9.g.vcf.gz.tbi, called/N_685.contig-group-9.g.vcf.gz.tbi, called/N_689.contig-group-9.g.vcf.gz.tbi, called/N_690.contig-group-9.g.vcf.gz.tbi, called/N_6926.contig-group-9.g.vcf.gz.tbi, called/N_6928.contig-group-9.g.vcf.gz.tbi, called/N_6932.contig-group-9.g.vcf.gz.tbi, called/N_6.contig-group-9.g.vcf.gz.tbi, called/N_7083.contig-group-9.g.vcf.gz.tbi, called/N_79.contig-group-9.g.vcf.gz.tbi, called/N_7.contig-group-9.g.vcf.gz.tbi, called/N_8105.contig-group-9.g.vcf.gz.tbi, called/N_8171.contig-group-9.g.vcf.gz.tbi, called/N_83.contig-group-9.g.vcf.gz.tbi, called/N_8564.contig-group-9.g.vcf.gz.tbi, called/N_8565.contig-group-9.g.vcf.gz.tbi, called/N_8583.contig-group-9.g.vcf.gz.tbi, called/N_8585.contig-group-9.g.vcf.gz.tbi, called/N_8586.contig-group-9.g.vcf.gz.tbi, called/N_9104.contig-group-9.g.vcf.gz.tbi, called/N_9449.contig-group-9.g.vcf.gz.tbi, called/N_94.contig-group-9.g.vcf.gz.tbi, called/T1481.contig-group-9.g.vcf.gz.tbi, called/T1483.contig-group-9.g.vcf.gz.tbi, called/T178.contig-group-9.g.vcf.gz.tbi, called/T179.contig-group-9.g.vcf.gz.tbi, called/T180.contig-group-9.g.vcf.gz.tbi, called/T181.contig-group-9.g.vcf.gz.tbi, called/T185.contig-group-9.g.vcf.gz.tbi, called/T186.contig-group-9.g.vcf.gz.tbi, called/T187.contig-group-9.g.vcf.gz.tbi, called/T188.contig-group-9.g.vcf.gz.tbi, called/T189.contig-group-9.g.vcf.gz.tbi, called/T190.contig-group-9.g.vcf.gz.tbi, called/T192.contig-group-9.g.vcf.gz.tbi, called/T193.contig-group-9.g.vcf.gz.tbi, called/T194.contig-group-9.g.vcf.gz.tbi, called/T196.contig-group-9.g.vcf.gz.tbi, called/T248.contig-group-9.g.vcf.gz.tbi, called/T37.contig-group-9.g.vcf.gz.tbi, called/T72.contig-group-9.g.vcf.gz.tbi, called/T79.contig-group-9.g.vcf.gz.tbi output: called/all.contig-group-9.g.vcf.gz, called/all.contig-group-9.g.done log: logs/gatk/combine-gvcfs/contig-group-9.log jobid: 2269 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-9.bench.log reason: Input files updated by another job: called/N_1156.contig-group-9.g.vcf.gz.tbi, called/N_1992_0123.contig-group-9.g.vcf.gz, called/N2005.contig-group-9.g.vcf.gz, called/N_4847.contig-group-9.g.vcf.gz.tbi, called/T185.contig-group-9.g.vcf.gz.tbi, called/N_4843.contig-group-9.g.vcf.gz.tbi, called/N_6490.contig-group-9.g.vcf.gz, called/N_1156.contig-group-9.g.vcf.gz, called/N_1870.contig-group-9.g.vcf.gz, called/N_1927.contig-group-9.g.vcf.gz.tbi, called/N_102.contig-group-9.g.vcf.gz, called/N_1870.contig-group-9.g.vcf.gz.tbi, called/N_6489.contig-group-9.g.vcf.gz.tbi, called/N_6490.contig-group-9.g.vcf.gz.tbi, called/N_4843.contig-group-9.g.vcf.gz, called/N_1354.contig-group-9.g.vcf.gz.tbi, called/N_5129.contig-group-9.g.vcf.gz.tbi, called/N_1992_0123.contig-group-9.g.vcf.gz.tbi, called/T187.contig-group-9.g.vcf.gz, called/M5672.contig-group-9.g.vcf.gz.tbi, called/M5672.contig-group-9.g.vcf.gz, called/N_1386.contig-group-9.g.vcf.gz.tbi, called/N_690.contig-group-9.g.vcf.gz, called/T180.contig-group-9.g.vcf.gz, called/N_690.contig-group-9.g.vcf.gz.tbi, called/T190.contig-group-9.g.vcf.gz.tbi, called/N_6928.contig-group-9.g.vcf.gz.tbi, called/N_1609.contig-group-9.g.vcf.gz.tbi, called/T72.contig-group-9.g.vcf.gz, called/T185.contig-group-9.g.vcf.gz, called/N_1158.contig-group-9.g.vcf.gz.tbi, called/N_1157.contig-group-9.g.vcf.gz.tbi, called/N_351.contig-group-9.g.vcf.gz, called/N_9104.contig-group-9.g.vcf.gz.tbi, called/N_8565.contig-group-9.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-9.g.vcf.gz.tbi, called/N_83.contig-group-9.g.vcf.gz.tbi, called/T187.contig-group-9.g.vcf.gz.tbi, called/N_1927.contig-group-9.g.vcf.gz, called/T192.contig-group-9.g.vcf.gz.tbi, called/T196.contig-group-9.g.vcf.gz, called/T79.contig-group-9.g.vcf.gz, called/N_1158.contig-group-9.g.vcf.gz, called/T192.contig-group-9.g.vcf.gz, called/N_351.contig-group-9.g.vcf.gz.tbi, called/T79.contig-group-9.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-9.g.vcf.gz, called/N_9449.contig-group-9.g.vcf.gz.tbi, called/N_2003_5409.contig-group-9.g.vcf.gz.tbi, called/N_1354.contig-group-9.g.vcf.gz, called/N_79.contig-group-9.g.vcf.gz, called/N_8583.contig-group-9.g.vcf.gz, called/N_79.contig-group-9.g.vcf.gz.tbi, called/N_689.contig-group-9.g.vcf.gz, called/N_4847.contig-group-9.g.vcf.gz, called/T1483.contig-group-9.g.vcf.gz.tbi, called/T196.contig-group-9.g.vcf.gz.tbi, called/N_102.contig-group-9.g.vcf.gz.tbi, called/N_8565.contig-group-9.g.vcf.gz, called/T190.contig-group-9.g.vcf.gz, called/T180.contig-group-9.g.vcf.gz.tbi, called/T72.contig-group-9.g.vcf.gz.tbi, called/T1483.contig-group-9.g.vcf.gz, called/N_9449.contig-group-9.g.vcf.gz, called/N_1157.contig-group-9.g.vcf.gz, called/N_9104.contig-group-9.g.vcf.gz, called/N_5129.contig-group-9.g.vcf.gz, called/N_8171.contig-group-9.g.vcf.gz.tbi, called/N_8583.contig-group-9.g.vcf.gz.tbi, called/N_6489.contig-group-9.g.vcf.gz, called/N2005.contig-group-9.g.vcf.gz.tbi, called/N_8171.contig-group-9.g.vcf.gz, called/N_2003_5409.contig-group-9.g.vcf.gz, called/N_689.contig-group-9.g.vcf.gz.tbi, called/N_1386.contig-group-9.g.vcf.gz, called/N_6928.contig-group-9.g.vcf.gz, called/N_83.contig-group-9.g.vcf.gz, called/N_1609.contig-group-9.g.vcf.gz wildcards: contig=contig-group-9 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-12.g.vcf.gz, called/M1865_2.contig-group-12.g.vcf.gz, called/M5672.contig-group-12.g.vcf.gz, called/MTDC48361.contig-group-12.g.vcf.gz, called/N2005.contig-group-12.g.vcf.gz, called/N_102.contig-group-12.g.vcf.gz, called/N_1085.contig-group-12.g.vcf.gz, called/N_1156.contig-group-12.g.vcf.gz, called/N_1157.contig-group-12.g.vcf.gz, called/N_1158.contig-group-12.g.vcf.gz, called/N_1344.contig-group-12.g.vcf.gz, called/N_1347.contig-group-12.g.vcf.gz, called/N_1354.contig-group-12.g.vcf.gz, called/N_1355.contig-group-12.g.vcf.gz, called/N_1384.contig-group-12.g.vcf.gz, called/N_1386.contig-group-12.g.vcf.gz, called/N_1390.contig-group-12.g.vcf.gz, called/N_1409.contig-group-12.g.vcf.gz, called/N_1411.contig-group-12.g.vcf.gz, called/N_1413.contig-group-12.g.vcf.gz, called/N_1414.contig-group-12.g.vcf.gz, called/N_1609.contig-group-12.g.vcf.gz, called/N_1870.contig-group-12.g.vcf.gz, called/N_1901.contig-group-12.g.vcf.gz, called/N_1913.contig-group-12.g.vcf.gz, called/N_1927.contig-group-12.g.vcf.gz, called/N_192.contig-group-12.g.vcf.gz, called/N_1934_1_1_368.contig-group-12.g.vcf.gz, called/N_1934_1_1_5973.contig-group-12.g.vcf.gz, called/N_1951_13_1951.contig-group-12.g.vcf.gz, called/N_1992_0123.contig-group-12.g.vcf.gz, called/N_1998_0130.contig-group-12.g.vcf.gz, called/N_2001_0025.contig-group-12.g.vcf.gz, called/N_2001_0205.contig-group-12.g.vcf.gz, called/N_2002_0292.contig-group-12.g.vcf.gz, called/N_2003_5409.contig-group-12.g.vcf.gz, called/N_2004.contig-group-12.g.vcf.gz, called/N_2010_1759.contig-group-12.g.vcf.gz, called/N_21.contig-group-12.g.vcf.gz, called/N_351.contig-group-12.g.vcf.gz, called/N_355.contig-group-12.g.vcf.gz, called/N_401.contig-group-12.g.vcf.gz, called/N_403.contig-group-12.g.vcf.gz, called/N_4843.contig-group-12.g.vcf.gz, called/N_4844.contig-group-12.g.vcf.gz, called/N_4846.contig-group-12.g.vcf.gz, called/N_4847.contig-group-12.g.vcf.gz, called/N_5056.contig-group-12.g.vcf.gz, called/N_5057.contig-group-12.g.vcf.gz, called/N_5129.contig-group-12.g.vcf.gz, called/N_6489.contig-group-12.g.vcf.gz, called/N_6490.contig-group-12.g.vcf.gz, called/N_685.contig-group-12.g.vcf.gz, called/N_689.contig-group-12.g.vcf.gz, called/N_690.contig-group-12.g.vcf.gz, called/N_6926.contig-group-12.g.vcf.gz, called/N_6928.contig-group-12.g.vcf.gz, called/N_6932.contig-group-12.g.vcf.gz, called/N_6.contig-group-12.g.vcf.gz, called/N_7083.contig-group-12.g.vcf.gz, called/N_79.contig-group-12.g.vcf.gz, called/N_7.contig-group-12.g.vcf.gz, called/N_8105.contig-group-12.g.vcf.gz, called/N_8171.contig-group-12.g.vcf.gz, called/N_83.contig-group-12.g.vcf.gz, called/N_8564.contig-group-12.g.vcf.gz, called/N_8565.contig-group-12.g.vcf.gz, called/N_8583.contig-group-12.g.vcf.gz, called/N_8585.contig-group-12.g.vcf.gz, called/N_8586.contig-group-12.g.vcf.gz, called/N_9104.contig-group-12.g.vcf.gz, called/N_9449.contig-group-12.g.vcf.gz, called/N_94.contig-group-12.g.vcf.gz, called/T1481.contig-group-12.g.vcf.gz, called/T1483.contig-group-12.g.vcf.gz, called/T178.contig-group-12.g.vcf.gz, called/T179.contig-group-12.g.vcf.gz, called/T180.contig-group-12.g.vcf.gz, called/T181.contig-group-12.g.vcf.gz, called/T185.contig-group-12.g.vcf.gz, called/T186.contig-group-12.g.vcf.gz, called/T187.contig-group-12.g.vcf.gz, called/T188.contig-group-12.g.vcf.gz, called/T189.contig-group-12.g.vcf.gz, called/T190.contig-group-12.g.vcf.gz, called/T192.contig-group-12.g.vcf.gz, called/T193.contig-group-12.g.vcf.gz, called/T194.contig-group-12.g.vcf.gz, called/T196.contig-group-12.g.vcf.gz, called/T248.contig-group-12.g.vcf.gz, called/T37.contig-group-12.g.vcf.gz, called/T72.contig-group-12.g.vcf.gz, called/T79.contig-group-12.g.vcf.gz, called/M1864_2.contig-group-12.g.vcf.gz.tbi, called/M1865_2.contig-group-12.g.vcf.gz.tbi, called/M5672.contig-group-12.g.vcf.gz.tbi, called/MTDC48361.contig-group-12.g.vcf.gz.tbi, called/N2005.contig-group-12.g.vcf.gz.tbi, called/N_102.contig-group-12.g.vcf.gz.tbi, called/N_1085.contig-group-12.g.vcf.gz.tbi, called/N_1156.contig-group-12.g.vcf.gz.tbi, called/N_1157.contig-group-12.g.vcf.gz.tbi, called/N_1158.contig-group-12.g.vcf.gz.tbi, called/N_1344.contig-group-12.g.vcf.gz.tbi, called/N_1347.contig-group-12.g.vcf.gz.tbi, called/N_1354.contig-group-12.g.vcf.gz.tbi, called/N_1355.contig-group-12.g.vcf.gz.tbi, called/N_1384.contig-group-12.g.vcf.gz.tbi, called/N_1386.contig-group-12.g.vcf.gz.tbi, called/N_1390.contig-group-12.g.vcf.gz.tbi, called/N_1409.contig-group-12.g.vcf.gz.tbi, called/N_1411.contig-group-12.g.vcf.gz.tbi, called/N_1413.contig-group-12.g.vcf.gz.tbi, called/N_1414.contig-group-12.g.vcf.gz.tbi, called/N_1609.contig-group-12.g.vcf.gz.tbi, called/N_1870.contig-group-12.g.vcf.gz.tbi, called/N_1901.contig-group-12.g.vcf.gz.tbi, called/N_1913.contig-group-12.g.vcf.gz.tbi, called/N_1927.contig-group-12.g.vcf.gz.tbi, called/N_192.contig-group-12.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-12.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-12.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-12.g.vcf.gz.tbi, called/N_1992_0123.contig-group-12.g.vcf.gz.tbi, called/N_1998_0130.contig-group-12.g.vcf.gz.tbi, called/N_2001_0025.contig-group-12.g.vcf.gz.tbi, called/N_2001_0205.contig-group-12.g.vcf.gz.tbi, called/N_2002_0292.contig-group-12.g.vcf.gz.tbi, called/N_2003_5409.contig-group-12.g.vcf.gz.tbi, called/N_2004.contig-group-12.g.vcf.gz.tbi, called/N_2010_1759.contig-group-12.g.vcf.gz.tbi, called/N_21.contig-group-12.g.vcf.gz.tbi, called/N_351.contig-group-12.g.vcf.gz.tbi, called/N_355.contig-group-12.g.vcf.gz.tbi, called/N_401.contig-group-12.g.vcf.gz.tbi, called/N_403.contig-group-12.g.vcf.gz.tbi, called/N_4843.contig-group-12.g.vcf.gz.tbi, called/N_4844.contig-group-12.g.vcf.gz.tbi, called/N_4846.contig-group-12.g.vcf.gz.tbi, called/N_4847.contig-group-12.g.vcf.gz.tbi, called/N_5056.contig-group-12.g.vcf.gz.tbi, called/N_5057.contig-group-12.g.vcf.gz.tbi, called/N_5129.contig-group-12.g.vcf.gz.tbi, called/N_6489.contig-group-12.g.vcf.gz.tbi, called/N_6490.contig-group-12.g.vcf.gz.tbi, called/N_685.contig-group-12.g.vcf.gz.tbi, called/N_689.contig-group-12.g.vcf.gz.tbi, called/N_690.contig-group-12.g.vcf.gz.tbi, called/N_6926.contig-group-12.g.vcf.gz.tbi, called/N_6928.contig-group-12.g.vcf.gz.tbi, called/N_6932.contig-group-12.g.vcf.gz.tbi, called/N_6.contig-group-12.g.vcf.gz.tbi, called/N_7083.contig-group-12.g.vcf.gz.tbi, called/N_79.contig-group-12.g.vcf.gz.tbi, called/N_7.contig-group-12.g.vcf.gz.tbi, called/N_8105.contig-group-12.g.vcf.gz.tbi, called/N_8171.contig-group-12.g.vcf.gz.tbi, called/N_83.contig-group-12.g.vcf.gz.tbi, called/N_8564.contig-group-12.g.vcf.gz.tbi, called/N_8565.contig-group-12.g.vcf.gz.tbi, called/N_8583.contig-group-12.g.vcf.gz.tbi, called/N_8585.contig-group-12.g.vcf.gz.tbi, called/N_8586.contig-group-12.g.vcf.gz.tbi, called/N_9104.contig-group-12.g.vcf.gz.tbi, called/N_9449.contig-group-12.g.vcf.gz.tbi, called/N_94.contig-group-12.g.vcf.gz.tbi, called/T1481.contig-group-12.g.vcf.gz.tbi, called/T1483.contig-group-12.g.vcf.gz.tbi, called/T178.contig-group-12.g.vcf.gz.tbi, called/T179.contig-group-12.g.vcf.gz.tbi, called/T180.contig-group-12.g.vcf.gz.tbi, called/T181.contig-group-12.g.vcf.gz.tbi, called/T185.contig-group-12.g.vcf.gz.tbi, called/T186.contig-group-12.g.vcf.gz.tbi, called/T187.contig-group-12.g.vcf.gz.tbi, called/T188.contig-group-12.g.vcf.gz.tbi, called/T189.contig-group-12.g.vcf.gz.tbi, called/T190.contig-group-12.g.vcf.gz.tbi, called/T192.contig-group-12.g.vcf.gz.tbi, called/T193.contig-group-12.g.vcf.gz.tbi, called/T194.contig-group-12.g.vcf.gz.tbi, called/T196.contig-group-12.g.vcf.gz.tbi, called/T248.contig-group-12.g.vcf.gz.tbi, called/T37.contig-group-12.g.vcf.gz.tbi, called/T72.contig-group-12.g.vcf.gz.tbi, called/T79.contig-group-12.g.vcf.gz.tbi output: called/all.contig-group-12.g.vcf.gz, called/all.contig-group-12.g.done log: logs/gatk/combine-gvcfs/contig-group-12.log jobid: 2557 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-12.bench.log reason: Input files updated by another job: called/M5672.contig-group-12.g.vcf.gz.tbi, called/N_5129.contig-group-12.g.vcf.gz.tbi, called/T1483.contig-group-12.g.vcf.gz, called/N2005.contig-group-12.g.vcf.gz, called/T72.contig-group-12.g.vcf.gz, called/N_1386.contig-group-12.g.vcf.gz.tbi, called/N_1609.contig-group-12.g.vcf.gz.tbi, called/N_1156.contig-group-12.g.vcf.gz.tbi, called/N_79.contig-group-12.g.vcf.gz.tbi, called/N_6490.contig-group-12.g.vcf.gz.tbi, called/N_689.contig-group-12.g.vcf.gz.tbi, called/N_1870.contig-group-12.g.vcf.gz, called/N_1354.contig-group-12.g.vcf.gz, called/N_1870.contig-group-12.g.vcf.gz.tbi, called/N_8171.contig-group-12.g.vcf.gz.tbi, called/N_690.contig-group-12.g.vcf.gz.tbi, called/N_6928.contig-group-12.g.vcf.gz.tbi, called/N_79.contig-group-12.g.vcf.gz, called/N_8171.contig-group-12.g.vcf.gz, called/N_9449.contig-group-12.g.vcf.gz.tbi, called/N_1157.contig-group-12.g.vcf.gz, called/T190.contig-group-12.g.vcf.gz, called/T196.contig-group-12.g.vcf.gz.tbi, called/N_83.contig-group-12.g.vcf.gz.tbi, called/N_1386.contig-group-12.g.vcf.gz, called/N_1992_0123.contig-group-12.g.vcf.gz, called/N_1934_1_1_5973.contig-group-12.g.vcf.gz.tbi, called/N_1927.contig-group-12.g.vcf.gz, called/N_4843.contig-group-12.g.vcf.gz.tbi, called/N_6928.contig-group-12.g.vcf.gz, called/T180.contig-group-12.g.vcf.gz, called/N_689.contig-group-12.g.vcf.gz, called/N_83.contig-group-12.g.vcf.gz, called/N_102.contig-group-12.g.vcf.gz.tbi, called/N_1927.contig-group-12.g.vcf.gz.tbi, called/N_4847.contig-group-12.g.vcf.gz.tbi, called/T187.contig-group-12.g.vcf.gz, called/N_2003_5409.contig-group-12.g.vcf.gz, called/N_9449.contig-group-12.g.vcf.gz, called/N_8583.contig-group-12.g.vcf.gz.tbi, called/N_1609.contig-group-12.g.vcf.gz, called/N_1992_0123.contig-group-12.g.vcf.gz.tbi, called/T79.contig-group-12.g.vcf.gz, called/N_9104.contig-group-12.g.vcf.gz.tbi, called/N_1158.contig-group-12.g.vcf.gz, called/N_102.contig-group-12.g.vcf.gz, called/N_6489.contig-group-12.g.vcf.gz, called/T192.contig-group-12.g.vcf.gz.tbi, called/N_1354.contig-group-12.g.vcf.gz.tbi, called/N_2003_5409.contig-group-12.g.vcf.gz.tbi, called/N_6489.contig-group-12.g.vcf.gz.tbi, called/N_4843.contig-group-12.g.vcf.gz, called/N_8565.contig-group-12.g.vcf.gz, called/N_690.contig-group-12.g.vcf.gz, called/N_351.contig-group-12.g.vcf.gz.tbi, called/N_6490.contig-group-12.g.vcf.gz, called/N_1934_1_1_5973.contig-group-12.g.vcf.gz, called/N_351.contig-group-12.g.vcf.gz, called/T192.contig-group-12.g.vcf.gz, called/N_1157.contig-group-12.g.vcf.gz.tbi, called/N_8583.contig-group-12.g.vcf.gz, called/N_1156.contig-group-12.g.vcf.gz, called/N_1158.contig-group-12.g.vcf.gz.tbi, called/M5672.contig-group-12.g.vcf.gz, called/T180.contig-group-12.g.vcf.gz.tbi, called/T185.contig-group-12.g.vcf.gz, called/T79.contig-group-12.g.vcf.gz.tbi, called/T185.contig-group-12.g.vcf.gz.tbi, called/T196.contig-group-12.g.vcf.gz, called/N2005.contig-group-12.g.vcf.gz.tbi, called/T190.contig-group-12.g.vcf.gz.tbi, called/N_5129.contig-group-12.g.vcf.gz, called/N_4847.contig-group-12.g.vcf.gz, called/N_9104.contig-group-12.g.vcf.gz, called/T1483.contig-group-12.g.vcf.gz.tbi, called/T72.contig-group-12.g.vcf.gz.tbi, called/T187.contig-group-12.g.vcf.gz.tbi, called/N_8565.contig-group-12.g.vcf.gz.tbi wildcards: contig=contig-group-12 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-21.g.vcf.gz, called/M1865_2.contig-group-21.g.vcf.gz, called/M5672.contig-group-21.g.vcf.gz, called/MTDC48361.contig-group-21.g.vcf.gz, called/N2005.contig-group-21.g.vcf.gz, called/N_102.contig-group-21.g.vcf.gz, called/N_1085.contig-group-21.g.vcf.gz, called/N_1156.contig-group-21.g.vcf.gz, called/N_1157.contig-group-21.g.vcf.gz, called/N_1158.contig-group-21.g.vcf.gz, called/N_1344.contig-group-21.g.vcf.gz, called/N_1347.contig-group-21.g.vcf.gz, called/N_1354.contig-group-21.g.vcf.gz, called/N_1355.contig-group-21.g.vcf.gz, called/N_1384.contig-group-21.g.vcf.gz, called/N_1386.contig-group-21.g.vcf.gz, called/N_1390.contig-group-21.g.vcf.gz, called/N_1409.contig-group-21.g.vcf.gz, called/N_1411.contig-group-21.g.vcf.gz, called/N_1413.contig-group-21.g.vcf.gz, called/N_1414.contig-group-21.g.vcf.gz, called/N_1609.contig-group-21.g.vcf.gz, called/N_1870.contig-group-21.g.vcf.gz, called/N_1901.contig-group-21.g.vcf.gz, called/N_1913.contig-group-21.g.vcf.gz, called/N_1927.contig-group-21.g.vcf.gz, called/N_192.contig-group-21.g.vcf.gz, called/N_1934_1_1_368.contig-group-21.g.vcf.gz, called/N_1934_1_1_5973.contig-group-21.g.vcf.gz, called/N_1951_13_1951.contig-group-21.g.vcf.gz, called/N_1992_0123.contig-group-21.g.vcf.gz, called/N_1998_0130.contig-group-21.g.vcf.gz, called/N_2001_0025.contig-group-21.g.vcf.gz, called/N_2001_0205.contig-group-21.g.vcf.gz, called/N_2002_0292.contig-group-21.g.vcf.gz, called/N_2003_5409.contig-group-21.g.vcf.gz, called/N_2004.contig-group-21.g.vcf.gz, called/N_2010_1759.contig-group-21.g.vcf.gz, called/N_21.contig-group-21.g.vcf.gz, called/N_351.contig-group-21.g.vcf.gz, called/N_355.contig-group-21.g.vcf.gz, called/N_401.contig-group-21.g.vcf.gz, called/N_403.contig-group-21.g.vcf.gz, called/N_4843.contig-group-21.g.vcf.gz, called/N_4844.contig-group-21.g.vcf.gz, called/N_4846.contig-group-21.g.vcf.gz, called/N_4847.contig-group-21.g.vcf.gz, called/N_5056.contig-group-21.g.vcf.gz, called/N_5057.contig-group-21.g.vcf.gz, called/N_5129.contig-group-21.g.vcf.gz, called/N_6489.contig-group-21.g.vcf.gz, called/N_6490.contig-group-21.g.vcf.gz, called/N_685.contig-group-21.g.vcf.gz, called/N_689.contig-group-21.g.vcf.gz, called/N_690.contig-group-21.g.vcf.gz, called/N_6926.contig-group-21.g.vcf.gz, called/N_6928.contig-group-21.g.vcf.gz, called/N_6932.contig-group-21.g.vcf.gz, called/N_6.contig-group-21.g.vcf.gz, called/N_7083.contig-group-21.g.vcf.gz, called/N_79.contig-group-21.g.vcf.gz, called/N_7.contig-group-21.g.vcf.gz, called/N_8105.contig-group-21.g.vcf.gz, called/N_8171.contig-group-21.g.vcf.gz, called/N_83.contig-group-21.g.vcf.gz, called/N_8564.contig-group-21.g.vcf.gz, called/N_8565.contig-group-21.g.vcf.gz, called/N_8583.contig-group-21.g.vcf.gz, called/N_8585.contig-group-21.g.vcf.gz, called/N_8586.contig-group-21.g.vcf.gz, called/N_9104.contig-group-21.g.vcf.gz, called/N_9449.contig-group-21.g.vcf.gz, called/N_94.contig-group-21.g.vcf.gz, called/T1481.contig-group-21.g.vcf.gz, called/T1483.contig-group-21.g.vcf.gz, called/T178.contig-group-21.g.vcf.gz, called/T179.contig-group-21.g.vcf.gz, called/T180.contig-group-21.g.vcf.gz, called/T181.contig-group-21.g.vcf.gz, called/T185.contig-group-21.g.vcf.gz, called/T186.contig-group-21.g.vcf.gz, called/T187.contig-group-21.g.vcf.gz, called/T188.contig-group-21.g.vcf.gz, called/T189.contig-group-21.g.vcf.gz, called/T190.contig-group-21.g.vcf.gz, called/T192.contig-group-21.g.vcf.gz, called/T193.contig-group-21.g.vcf.gz, called/T194.contig-group-21.g.vcf.gz, called/T196.contig-group-21.g.vcf.gz, called/T248.contig-group-21.g.vcf.gz, called/T37.contig-group-21.g.vcf.gz, called/T72.contig-group-21.g.vcf.gz, called/T79.contig-group-21.g.vcf.gz, called/M1864_2.contig-group-21.g.vcf.gz.tbi, called/M1865_2.contig-group-21.g.vcf.gz.tbi, called/M5672.contig-group-21.g.vcf.gz.tbi, called/MTDC48361.contig-group-21.g.vcf.gz.tbi, called/N2005.contig-group-21.g.vcf.gz.tbi, called/N_102.contig-group-21.g.vcf.gz.tbi, called/N_1085.contig-group-21.g.vcf.gz.tbi, called/N_1156.contig-group-21.g.vcf.gz.tbi, called/N_1157.contig-group-21.g.vcf.gz.tbi, called/N_1158.contig-group-21.g.vcf.gz.tbi, called/N_1344.contig-group-21.g.vcf.gz.tbi, called/N_1347.contig-group-21.g.vcf.gz.tbi, called/N_1354.contig-group-21.g.vcf.gz.tbi, called/N_1355.contig-group-21.g.vcf.gz.tbi, called/N_1384.contig-group-21.g.vcf.gz.tbi, called/N_1386.contig-group-21.g.vcf.gz.tbi, called/N_1390.contig-group-21.g.vcf.gz.tbi, called/N_1409.contig-group-21.g.vcf.gz.tbi, called/N_1411.contig-group-21.g.vcf.gz.tbi, called/N_1413.contig-group-21.g.vcf.gz.tbi, called/N_1414.contig-group-21.g.vcf.gz.tbi, called/N_1609.contig-group-21.g.vcf.gz.tbi, called/N_1870.contig-group-21.g.vcf.gz.tbi, called/N_1901.contig-group-21.g.vcf.gz.tbi, called/N_1913.contig-group-21.g.vcf.gz.tbi, called/N_1927.contig-group-21.g.vcf.gz.tbi, called/N_192.contig-group-21.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-21.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-21.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-21.g.vcf.gz.tbi, called/N_1992_0123.contig-group-21.g.vcf.gz.tbi, called/N_1998_0130.contig-group-21.g.vcf.gz.tbi, called/N_2001_0025.contig-group-21.g.vcf.gz.tbi, called/N_2001_0205.contig-group-21.g.vcf.gz.tbi, called/N_2002_0292.contig-group-21.g.vcf.gz.tbi, called/N_2003_5409.contig-group-21.g.vcf.gz.tbi, called/N_2004.contig-group-21.g.vcf.gz.tbi, called/N_2010_1759.contig-group-21.g.vcf.gz.tbi, called/N_21.contig-group-21.g.vcf.gz.tbi, called/N_351.contig-group-21.g.vcf.gz.tbi, called/N_355.contig-group-21.g.vcf.gz.tbi, called/N_401.contig-group-21.g.vcf.gz.tbi, called/N_403.contig-group-21.g.vcf.gz.tbi, called/N_4843.contig-group-21.g.vcf.gz.tbi, called/N_4844.contig-group-21.g.vcf.gz.tbi, called/N_4846.contig-group-21.g.vcf.gz.tbi, called/N_4847.contig-group-21.g.vcf.gz.tbi, called/N_5056.contig-group-21.g.vcf.gz.tbi, called/N_5057.contig-group-21.g.vcf.gz.tbi, called/N_5129.contig-group-21.g.vcf.gz.tbi, called/N_6489.contig-group-21.g.vcf.gz.tbi, called/N_6490.contig-group-21.g.vcf.gz.tbi, called/N_685.contig-group-21.g.vcf.gz.tbi, called/N_689.contig-group-21.g.vcf.gz.tbi, called/N_690.contig-group-21.g.vcf.gz.tbi, called/N_6926.contig-group-21.g.vcf.gz.tbi, called/N_6928.contig-group-21.g.vcf.gz.tbi, called/N_6932.contig-group-21.g.vcf.gz.tbi, called/N_6.contig-group-21.g.vcf.gz.tbi, called/N_7083.contig-group-21.g.vcf.gz.tbi, called/N_79.contig-group-21.g.vcf.gz.tbi, called/N_7.contig-group-21.g.vcf.gz.tbi, called/N_8105.contig-group-21.g.vcf.gz.tbi, called/N_8171.contig-group-21.g.vcf.gz.tbi, called/N_83.contig-group-21.g.vcf.gz.tbi, called/N_8564.contig-group-21.g.vcf.gz.tbi, called/N_8565.contig-group-21.g.vcf.gz.tbi, called/N_8583.contig-group-21.g.vcf.gz.tbi, called/N_8585.contig-group-21.g.vcf.gz.tbi, called/N_8586.contig-group-21.g.vcf.gz.tbi, called/N_9104.contig-group-21.g.vcf.gz.tbi, called/N_9449.contig-group-21.g.vcf.gz.tbi, called/N_94.contig-group-21.g.vcf.gz.tbi, called/T1481.contig-group-21.g.vcf.gz.tbi, called/T1483.contig-group-21.g.vcf.gz.tbi, called/T178.contig-group-21.g.vcf.gz.tbi, called/T179.contig-group-21.g.vcf.gz.tbi, called/T180.contig-group-21.g.vcf.gz.tbi, called/T181.contig-group-21.g.vcf.gz.tbi, called/T185.contig-group-21.g.vcf.gz.tbi, called/T186.contig-group-21.g.vcf.gz.tbi, called/T187.contig-group-21.g.vcf.gz.tbi, called/T188.contig-group-21.g.vcf.gz.tbi, called/T189.contig-group-21.g.vcf.gz.tbi, called/T190.contig-group-21.g.vcf.gz.tbi, called/T192.contig-group-21.g.vcf.gz.tbi, called/T193.contig-group-21.g.vcf.gz.tbi, called/T194.contig-group-21.g.vcf.gz.tbi, called/T196.contig-group-21.g.vcf.gz.tbi, called/T248.contig-group-21.g.vcf.gz.tbi, called/T37.contig-group-21.g.vcf.gz.tbi, called/T72.contig-group-21.g.vcf.gz.tbi, called/T79.contig-group-21.g.vcf.gz.tbi output: called/all.contig-group-21.g.vcf.gz, called/all.contig-group-21.g.done log: logs/gatk/combine-gvcfs/contig-group-21.log jobid: 3421 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-21.bench.log reason: Input files updated by another job: called/N_8565.contig-group-21.g.vcf.gz.tbi, called/N_9449.contig-group-21.g.vcf.gz.tbi, called/N_1156.contig-group-21.g.vcf.gz, called/T190.contig-group-21.g.vcf.gz, called/N_5129.contig-group-21.g.vcf.gz, called/N_1927.contig-group-21.g.vcf.gz, called/N_689.contig-group-21.g.vcf.gz, called/N_2003_5409.contig-group-21.g.vcf.gz.tbi, called/N_8583.contig-group-21.g.vcf.gz.tbi, called/N_690.contig-group-21.g.vcf.gz.tbi, called/T196.contig-group-21.g.vcf.gz.tbi, called/N_4843.contig-group-21.g.vcf.gz.tbi, called/T79.contig-group-21.g.vcf.gz, called/N2005.contig-group-21.g.vcf.gz.tbi, called/N_1927.contig-group-21.g.vcf.gz.tbi, called/N_4847.contig-group-21.g.vcf.gz.tbi, called/N_102.contig-group-21.g.vcf.gz, called/N_6490.contig-group-21.g.vcf.gz.tbi, called/N_5129.contig-group-21.g.vcf.gz.tbi, called/N_8565.contig-group-21.g.vcf.gz, called/N_2003_5409.contig-group-21.g.vcf.gz, called/T1483.contig-group-21.g.vcf.gz, called/N_9449.contig-group-21.g.vcf.gz, called/N_1354.contig-group-21.g.vcf.gz.tbi, called/N_351.contig-group-21.g.vcf.gz, called/T196.contig-group-21.g.vcf.gz, called/T192.contig-group-21.g.vcf.gz.tbi, called/N_1354.contig-group-21.g.vcf.gz, called/N_1157.contig-group-21.g.vcf.gz, called/N_79.contig-group-21.g.vcf.gz, called/T192.contig-group-21.g.vcf.gz, called/N_4843.contig-group-21.g.vcf.gz, called/N_1386.contig-group-21.g.vcf.gz, called/N_1609.contig-group-21.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-21.g.vcf.gz.tbi, called/N_83.contig-group-21.g.vcf.gz.tbi, called/N_1157.contig-group-21.g.vcf.gz.tbi, called/N_83.contig-group-21.g.vcf.gz, called/N_1158.contig-group-21.g.vcf.gz, called/N_690.contig-group-21.g.vcf.gz, called/N_351.contig-group-21.g.vcf.gz.tbi, called/M5672.contig-group-21.g.vcf.gz, called/N_8171.contig-group-21.g.vcf.gz.tbi, called/T79.contig-group-21.g.vcf.gz.tbi, called/T187.contig-group-21.g.vcf.gz, called/N_1992_0123.contig-group-21.g.vcf.gz.tbi, called/N_102.contig-group-21.g.vcf.gz.tbi, called/T185.contig-group-21.g.vcf.gz, called/T190.contig-group-21.g.vcf.gz.tbi, called/N_79.contig-group-21.g.vcf.gz.tbi, called/N_9104.contig-group-21.g.vcf.gz.tbi, called/N_1992_0123.contig-group-21.g.vcf.gz, called/N_6928.contig-group-21.g.vcf.gz.tbi, called/N_1609.contig-group-21.g.vcf.gz, called/T180.contig-group-21.g.vcf.gz.tbi, called/N_1156.contig-group-21.g.vcf.gz.tbi, called/N_1158.contig-group-21.g.vcf.gz.tbi, called/T180.contig-group-21.g.vcf.gz, called/T72.contig-group-21.g.vcf.gz.tbi, called/N_6489.contig-group-21.g.vcf.gz.tbi, called/N_689.contig-group-21.g.vcf.gz.tbi, called/N_1386.contig-group-21.g.vcf.gz.tbi, called/T187.contig-group-21.g.vcf.gz.tbi, called/M5672.contig-group-21.g.vcf.gz.tbi, called/T185.contig-group-21.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-21.g.vcf.gz, called/N_6489.contig-group-21.g.vcf.gz, called/N_6928.contig-group-21.g.vcf.gz, called/T72.contig-group-21.g.vcf.gz, called/N2005.contig-group-21.g.vcf.gz, called/N_4847.contig-group-21.g.vcf.gz, called/N_6490.contig-group-21.g.vcf.gz, called/N_9104.contig-group-21.g.vcf.gz, called/N_1870.contig-group-21.g.vcf.gz.tbi, called/N_8583.contig-group-21.g.vcf.gz, called/N_1870.contig-group-21.g.vcf.gz, called/T1483.contig-group-21.g.vcf.gz.tbi, called/N_8171.contig-group-21.g.vcf.gz wildcards: contig=contig-group-21 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-14.g.vcf.gz, called/M1865_2.contig-group-14.g.vcf.gz, called/M5672.contig-group-14.g.vcf.gz, called/MTDC48361.contig-group-14.g.vcf.gz, called/N2005.contig-group-14.g.vcf.gz, called/N_102.contig-group-14.g.vcf.gz, called/N_1085.contig-group-14.g.vcf.gz, called/N_1156.contig-group-14.g.vcf.gz, called/N_1157.contig-group-14.g.vcf.gz, called/N_1158.contig-group-14.g.vcf.gz, called/N_1344.contig-group-14.g.vcf.gz, called/N_1347.contig-group-14.g.vcf.gz, called/N_1354.contig-group-14.g.vcf.gz, called/N_1355.contig-group-14.g.vcf.gz, called/N_1384.contig-group-14.g.vcf.gz, called/N_1386.contig-group-14.g.vcf.gz, called/N_1390.contig-group-14.g.vcf.gz, called/N_1409.contig-group-14.g.vcf.gz, called/N_1411.contig-group-14.g.vcf.gz, called/N_1413.contig-group-14.g.vcf.gz, called/N_1414.contig-group-14.g.vcf.gz, called/N_1609.contig-group-14.g.vcf.gz, called/N_1870.contig-group-14.g.vcf.gz, called/N_1901.contig-group-14.g.vcf.gz, called/N_1913.contig-group-14.g.vcf.gz, called/N_1927.contig-group-14.g.vcf.gz, called/N_192.contig-group-14.g.vcf.gz, called/N_1934_1_1_368.contig-group-14.g.vcf.gz, called/N_1934_1_1_5973.contig-group-14.g.vcf.gz, called/N_1951_13_1951.contig-group-14.g.vcf.gz, called/N_1992_0123.contig-group-14.g.vcf.gz, called/N_1998_0130.contig-group-14.g.vcf.gz, called/N_2001_0025.contig-group-14.g.vcf.gz, called/N_2001_0205.contig-group-14.g.vcf.gz, called/N_2002_0292.contig-group-14.g.vcf.gz, called/N_2003_5409.contig-group-14.g.vcf.gz, called/N_2004.contig-group-14.g.vcf.gz, called/N_2010_1759.contig-group-14.g.vcf.gz, called/N_21.contig-group-14.g.vcf.gz, called/N_351.contig-group-14.g.vcf.gz, called/N_355.contig-group-14.g.vcf.gz, called/N_401.contig-group-14.g.vcf.gz, called/N_403.contig-group-14.g.vcf.gz, called/N_4843.contig-group-14.g.vcf.gz, called/N_4844.contig-group-14.g.vcf.gz, called/N_4846.contig-group-14.g.vcf.gz, called/N_4847.contig-group-14.g.vcf.gz, called/N_5056.contig-group-14.g.vcf.gz, called/N_5057.contig-group-14.g.vcf.gz, called/N_5129.contig-group-14.g.vcf.gz, called/N_6489.contig-group-14.g.vcf.gz, called/N_6490.contig-group-14.g.vcf.gz, called/N_685.contig-group-14.g.vcf.gz, called/N_689.contig-group-14.g.vcf.gz, called/N_690.contig-group-14.g.vcf.gz, called/N_6926.contig-group-14.g.vcf.gz, called/N_6928.contig-group-14.g.vcf.gz, called/N_6932.contig-group-14.g.vcf.gz, called/N_6.contig-group-14.g.vcf.gz, called/N_7083.contig-group-14.g.vcf.gz, called/N_79.contig-group-14.g.vcf.gz, called/N_7.contig-group-14.g.vcf.gz, called/N_8105.contig-group-14.g.vcf.gz, called/N_8171.contig-group-14.g.vcf.gz, called/N_83.contig-group-14.g.vcf.gz, called/N_8564.contig-group-14.g.vcf.gz, called/N_8565.contig-group-14.g.vcf.gz, called/N_8583.contig-group-14.g.vcf.gz, called/N_8585.contig-group-14.g.vcf.gz, called/N_8586.contig-group-14.g.vcf.gz, called/N_9104.contig-group-14.g.vcf.gz, called/N_9449.contig-group-14.g.vcf.gz, called/N_94.contig-group-14.g.vcf.gz, called/T1481.contig-group-14.g.vcf.gz, called/T1483.contig-group-14.g.vcf.gz, called/T178.contig-group-14.g.vcf.gz, called/T179.contig-group-14.g.vcf.gz, called/T180.contig-group-14.g.vcf.gz, called/T181.contig-group-14.g.vcf.gz, called/T185.contig-group-14.g.vcf.gz, called/T186.contig-group-14.g.vcf.gz, called/T187.contig-group-14.g.vcf.gz, called/T188.contig-group-14.g.vcf.gz, called/T189.contig-group-14.g.vcf.gz, called/T190.contig-group-14.g.vcf.gz, called/T192.contig-group-14.g.vcf.gz, called/T193.contig-group-14.g.vcf.gz, called/T194.contig-group-14.g.vcf.gz, called/T196.contig-group-14.g.vcf.gz, called/T248.contig-group-14.g.vcf.gz, called/T37.contig-group-14.g.vcf.gz, called/T72.contig-group-14.g.vcf.gz, called/T79.contig-group-14.g.vcf.gz, called/M1864_2.contig-group-14.g.vcf.gz.tbi, called/M1865_2.contig-group-14.g.vcf.gz.tbi, called/M5672.contig-group-14.g.vcf.gz.tbi, called/MTDC48361.contig-group-14.g.vcf.gz.tbi, called/N2005.contig-group-14.g.vcf.gz.tbi, called/N_102.contig-group-14.g.vcf.gz.tbi, called/N_1085.contig-group-14.g.vcf.gz.tbi, called/N_1156.contig-group-14.g.vcf.gz.tbi, called/N_1157.contig-group-14.g.vcf.gz.tbi, called/N_1158.contig-group-14.g.vcf.gz.tbi, called/N_1344.contig-group-14.g.vcf.gz.tbi, called/N_1347.contig-group-14.g.vcf.gz.tbi, called/N_1354.contig-group-14.g.vcf.gz.tbi, called/N_1355.contig-group-14.g.vcf.gz.tbi, called/N_1384.contig-group-14.g.vcf.gz.tbi, called/N_1386.contig-group-14.g.vcf.gz.tbi, called/N_1390.contig-group-14.g.vcf.gz.tbi, called/N_1409.contig-group-14.g.vcf.gz.tbi, called/N_1411.contig-group-14.g.vcf.gz.tbi, called/N_1413.contig-group-14.g.vcf.gz.tbi, called/N_1414.contig-group-14.g.vcf.gz.tbi, called/N_1609.contig-group-14.g.vcf.gz.tbi, called/N_1870.contig-group-14.g.vcf.gz.tbi, called/N_1901.contig-group-14.g.vcf.gz.tbi, called/N_1913.contig-group-14.g.vcf.gz.tbi, called/N_1927.contig-group-14.g.vcf.gz.tbi, called/N_192.contig-group-14.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-14.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-14.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-14.g.vcf.gz.tbi, called/N_1992_0123.contig-group-14.g.vcf.gz.tbi, called/N_1998_0130.contig-group-14.g.vcf.gz.tbi, called/N_2001_0025.contig-group-14.g.vcf.gz.tbi, called/N_2001_0205.contig-group-14.g.vcf.gz.tbi, called/N_2002_0292.contig-group-14.g.vcf.gz.tbi, called/N_2003_5409.contig-group-14.g.vcf.gz.tbi, called/N_2004.contig-group-14.g.vcf.gz.tbi, called/N_2010_1759.contig-group-14.g.vcf.gz.tbi, called/N_21.contig-group-14.g.vcf.gz.tbi, called/N_351.contig-group-14.g.vcf.gz.tbi, called/N_355.contig-group-14.g.vcf.gz.tbi, called/N_401.contig-group-14.g.vcf.gz.tbi, called/N_403.contig-group-14.g.vcf.gz.tbi, called/N_4843.contig-group-14.g.vcf.gz.tbi, called/N_4844.contig-group-14.g.vcf.gz.tbi, called/N_4846.contig-group-14.g.vcf.gz.tbi, called/N_4847.contig-group-14.g.vcf.gz.tbi, called/N_5056.contig-group-14.g.vcf.gz.tbi, called/N_5057.contig-group-14.g.vcf.gz.tbi, called/N_5129.contig-group-14.g.vcf.gz.tbi, called/N_6489.contig-group-14.g.vcf.gz.tbi, called/N_6490.contig-group-14.g.vcf.gz.tbi, called/N_685.contig-group-14.g.vcf.gz.tbi, called/N_689.contig-group-14.g.vcf.gz.tbi, called/N_690.contig-group-14.g.vcf.gz.tbi, called/N_6926.contig-group-14.g.vcf.gz.tbi, called/N_6928.contig-group-14.g.vcf.gz.tbi, called/N_6932.contig-group-14.g.vcf.gz.tbi, called/N_6.contig-group-14.g.vcf.gz.tbi, called/N_7083.contig-group-14.g.vcf.gz.tbi, called/N_79.contig-group-14.g.vcf.gz.tbi, called/N_7.contig-group-14.g.vcf.gz.tbi, called/N_8105.contig-group-14.g.vcf.gz.tbi, called/N_8171.contig-group-14.g.vcf.gz.tbi, called/N_83.contig-group-14.g.vcf.gz.tbi, called/N_8564.contig-group-14.g.vcf.gz.tbi, called/N_8565.contig-group-14.g.vcf.gz.tbi, called/N_8583.contig-group-14.g.vcf.gz.tbi, called/N_8585.contig-group-14.g.vcf.gz.tbi, called/N_8586.contig-group-14.g.vcf.gz.tbi, called/N_9104.contig-group-14.g.vcf.gz.tbi, called/N_9449.contig-group-14.g.vcf.gz.tbi, called/N_94.contig-group-14.g.vcf.gz.tbi, called/T1481.contig-group-14.g.vcf.gz.tbi, called/T1483.contig-group-14.g.vcf.gz.tbi, called/T178.contig-group-14.g.vcf.gz.tbi, called/T179.contig-group-14.g.vcf.gz.tbi, called/T180.contig-group-14.g.vcf.gz.tbi, called/T181.contig-group-14.g.vcf.gz.tbi, called/T185.contig-group-14.g.vcf.gz.tbi, called/T186.contig-group-14.g.vcf.gz.tbi, called/T187.contig-group-14.g.vcf.gz.tbi, called/T188.contig-group-14.g.vcf.gz.tbi, called/T189.contig-group-14.g.vcf.gz.tbi, called/T190.contig-group-14.g.vcf.gz.tbi, called/T192.contig-group-14.g.vcf.gz.tbi, called/T193.contig-group-14.g.vcf.gz.tbi, called/T194.contig-group-14.g.vcf.gz.tbi, called/T196.contig-group-14.g.vcf.gz.tbi, called/T248.contig-group-14.g.vcf.gz.tbi, called/T37.contig-group-14.g.vcf.gz.tbi, called/T72.contig-group-14.g.vcf.gz.tbi, called/T79.contig-group-14.g.vcf.gz.tbi output: called/all.contig-group-14.g.vcf.gz, called/all.contig-group-14.g.done log: logs/gatk/combine-gvcfs/contig-group-14.log jobid: 2749 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-14.bench.log reason: Input files updated by another job: called/T72.contig-group-14.g.vcf.gz.tbi, called/N_1158.contig-group-14.g.vcf.gz, called/M5672.contig-group-14.g.vcf.gz.tbi, called/T192.contig-group-14.g.vcf.gz.tbi, called/T72.contig-group-14.g.vcf.gz, called/N_4843.contig-group-14.g.vcf.gz.tbi, called/N_351.contig-group-14.g.vcf.gz.tbi, called/T1483.contig-group-14.g.vcf.gz.tbi, called/N_1354.contig-group-14.g.vcf.gz.tbi, called/N_6928.contig-group-14.g.vcf.gz.tbi, called/T185.contig-group-14.g.vcf.gz, called/N_102.contig-group-14.g.vcf.gz, called/N_5129.contig-group-14.g.vcf.gz, called/N_83.contig-group-14.g.vcf.gz.tbi, called/N_1158.contig-group-14.g.vcf.gz.tbi, called/N_4847.contig-group-14.g.vcf.gz.tbi, called/N_9104.contig-group-14.g.vcf.gz, called/N_689.contig-group-14.g.vcf.gz.tbi, called/N_1354.contig-group-14.g.vcf.gz, called/T185.contig-group-14.g.vcf.gz.tbi, called/T192.contig-group-14.g.vcf.gz, called/N_2003_5409.contig-group-14.g.vcf.gz.tbi, called/N_1156.contig-group-14.g.vcf.gz, called/N_1934_1_1_5973.contig-group-14.g.vcf.gz.tbi, called/N_690.contig-group-14.g.vcf.gz.tbi, called/N_8565.contig-group-14.g.vcf.gz.tbi, called/T1483.contig-group-14.g.vcf.gz, called/N_1157.contig-group-14.g.vcf.gz.tbi, called/N2005.contig-group-14.g.vcf.gz.tbi, called/T190.contig-group-14.g.vcf.gz.tbi, called/N_1927.contig-group-14.g.vcf.gz, called/N_5129.contig-group-14.g.vcf.gz.tbi, called/N2005.contig-group-14.g.vcf.gz, called/T180.contig-group-14.g.vcf.gz.tbi, called/N_8583.contig-group-14.g.vcf.gz, called/N_6928.contig-group-14.g.vcf.gz, called/N_351.contig-group-14.g.vcf.gz, called/N_1992_0123.contig-group-14.g.vcf.gz.tbi, called/N_690.contig-group-14.g.vcf.gz, called/N_1927.contig-group-14.g.vcf.gz.tbi, called/T196.contig-group-14.g.vcf.gz, called/N_2003_5409.contig-group-14.g.vcf.gz, called/N_4847.contig-group-14.g.vcf.gz, called/N_6489.contig-group-14.g.vcf.gz.tbi, called/N_9104.contig-group-14.g.vcf.gz.tbi, called/N_8583.contig-group-14.g.vcf.gz.tbi, called/N_1870.contig-group-14.g.vcf.gz, called/T187.contig-group-14.g.vcf.gz.tbi, called/T180.contig-group-14.g.vcf.gz, called/N_1870.contig-group-14.g.vcf.gz.tbi, called/N_1156.contig-group-14.g.vcf.gz.tbi, called/N_6490.contig-group-14.g.vcf.gz.tbi, called/N_8565.contig-group-14.g.vcf.gz, called/T187.contig-group-14.g.vcf.gz, called/T196.contig-group-14.g.vcf.gz.tbi, called/M5672.contig-group-14.g.vcf.gz, called/N_9449.contig-group-14.g.vcf.gz, called/N_689.contig-group-14.g.vcf.gz, called/N_102.contig-group-14.g.vcf.gz.tbi, called/N_1992_0123.contig-group-14.g.vcf.gz, called/N_79.contig-group-14.g.vcf.gz, called/N_6490.contig-group-14.g.vcf.gz, called/N_1934_1_1_5973.contig-group-14.g.vcf.gz, called/N_1157.contig-group-14.g.vcf.gz, called/N_1386.contig-group-14.g.vcf.gz.tbi, called/N_4843.contig-group-14.g.vcf.gz, called/N_79.contig-group-14.g.vcf.gz.tbi, called/N_1609.contig-group-14.g.vcf.gz, called/N_1386.contig-group-14.g.vcf.gz, called/N_83.contig-group-14.g.vcf.gz, called/N_1609.contig-group-14.g.vcf.gz.tbi, called/N_8171.contig-group-14.g.vcf.gz, called/N_8171.contig-group-14.g.vcf.gz.tbi, called/N_6489.contig-group-14.g.vcf.gz, called/T190.contig-group-14.g.vcf.gz, called/T79.contig-group-14.g.vcf.gz.tbi, called/T79.contig-group-14.g.vcf.gz, called/N_9449.contig-group-14.g.vcf.gz.tbi wildcards: contig=contig-group-14 [Mon Jul 29 13:38:43 2024] rule combine_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/M1864_2.contig-group-5.g.vcf.gz, called/M1865_2.contig-group-5.g.vcf.gz, called/M5672.contig-group-5.g.vcf.gz, called/MTDC48361.contig-group-5.g.vcf.gz, called/N2005.contig-group-5.g.vcf.gz, called/N_102.contig-group-5.g.vcf.gz, called/N_1085.contig-group-5.g.vcf.gz, called/N_1156.contig-group-5.g.vcf.gz, called/N_1157.contig-group-5.g.vcf.gz, called/N_1158.contig-group-5.g.vcf.gz, called/N_1344.contig-group-5.g.vcf.gz, called/N_1347.contig-group-5.g.vcf.gz, called/N_1354.contig-group-5.g.vcf.gz, called/N_1355.contig-group-5.g.vcf.gz, called/N_1384.contig-group-5.g.vcf.gz, called/N_1386.contig-group-5.g.vcf.gz, called/N_1390.contig-group-5.g.vcf.gz, called/N_1409.contig-group-5.g.vcf.gz, called/N_1411.contig-group-5.g.vcf.gz, called/N_1413.contig-group-5.g.vcf.gz, called/N_1414.contig-group-5.g.vcf.gz, called/N_1609.contig-group-5.g.vcf.gz, called/N_1870.contig-group-5.g.vcf.gz, called/N_1901.contig-group-5.g.vcf.gz, called/N_1913.contig-group-5.g.vcf.gz, called/N_1927.contig-group-5.g.vcf.gz, called/N_192.contig-group-5.g.vcf.gz, called/N_1934_1_1_368.contig-group-5.g.vcf.gz, called/N_1934_1_1_5973.contig-group-5.g.vcf.gz, called/N_1951_13_1951.contig-group-5.g.vcf.gz, called/N_1992_0123.contig-group-5.g.vcf.gz, called/N_1998_0130.contig-group-5.g.vcf.gz, called/N_2001_0025.contig-group-5.g.vcf.gz, called/N_2001_0205.contig-group-5.g.vcf.gz, called/N_2002_0292.contig-group-5.g.vcf.gz, called/N_2003_5409.contig-group-5.g.vcf.gz, called/N_2004.contig-group-5.g.vcf.gz, called/N_2010_1759.contig-group-5.g.vcf.gz, called/N_21.contig-group-5.g.vcf.gz, called/N_351.contig-group-5.g.vcf.gz, called/N_355.contig-group-5.g.vcf.gz, called/N_401.contig-group-5.g.vcf.gz, called/N_403.contig-group-5.g.vcf.gz, called/N_4843.contig-group-5.g.vcf.gz, called/N_4844.contig-group-5.g.vcf.gz, called/N_4846.contig-group-5.g.vcf.gz, called/N_4847.contig-group-5.g.vcf.gz, called/N_5056.contig-group-5.g.vcf.gz, called/N_5057.contig-group-5.g.vcf.gz, called/N_5129.contig-group-5.g.vcf.gz, called/N_6489.contig-group-5.g.vcf.gz, called/N_6490.contig-group-5.g.vcf.gz, called/N_685.contig-group-5.g.vcf.gz, called/N_689.contig-group-5.g.vcf.gz, called/N_690.contig-group-5.g.vcf.gz, called/N_6926.contig-group-5.g.vcf.gz, called/N_6928.contig-group-5.g.vcf.gz, called/N_6932.contig-group-5.g.vcf.gz, called/N_6.contig-group-5.g.vcf.gz, called/N_7083.contig-group-5.g.vcf.gz, called/N_79.contig-group-5.g.vcf.gz, called/N_7.contig-group-5.g.vcf.gz, called/N_8105.contig-group-5.g.vcf.gz, called/N_8171.contig-group-5.g.vcf.gz, called/N_83.contig-group-5.g.vcf.gz, called/N_8564.contig-group-5.g.vcf.gz, called/N_8565.contig-group-5.g.vcf.gz, called/N_8583.contig-group-5.g.vcf.gz, called/N_8585.contig-group-5.g.vcf.gz, called/N_8586.contig-group-5.g.vcf.gz, called/N_9104.contig-group-5.g.vcf.gz, called/N_9449.contig-group-5.g.vcf.gz, called/N_94.contig-group-5.g.vcf.gz, called/T1481.contig-group-5.g.vcf.gz, called/T1483.contig-group-5.g.vcf.gz, called/T178.contig-group-5.g.vcf.gz, called/T179.contig-group-5.g.vcf.gz, called/T180.contig-group-5.g.vcf.gz, called/T181.contig-group-5.g.vcf.gz, called/T185.contig-group-5.g.vcf.gz, called/T186.contig-group-5.g.vcf.gz, called/T187.contig-group-5.g.vcf.gz, called/T188.contig-group-5.g.vcf.gz, called/T189.contig-group-5.g.vcf.gz, called/T190.contig-group-5.g.vcf.gz, called/T192.contig-group-5.g.vcf.gz, called/T193.contig-group-5.g.vcf.gz, called/T194.contig-group-5.g.vcf.gz, called/T196.contig-group-5.g.vcf.gz, called/T248.contig-group-5.g.vcf.gz, called/T37.contig-group-5.g.vcf.gz, called/T72.contig-group-5.g.vcf.gz, called/T79.contig-group-5.g.vcf.gz, called/M1864_2.contig-group-5.g.vcf.gz.tbi, called/M1865_2.contig-group-5.g.vcf.gz.tbi, called/M5672.contig-group-5.g.vcf.gz.tbi, called/MTDC48361.contig-group-5.g.vcf.gz.tbi, called/N2005.contig-group-5.g.vcf.gz.tbi, called/N_102.contig-group-5.g.vcf.gz.tbi, called/N_1085.contig-group-5.g.vcf.gz.tbi, called/N_1156.contig-group-5.g.vcf.gz.tbi, called/N_1157.contig-group-5.g.vcf.gz.tbi, called/N_1158.contig-group-5.g.vcf.gz.tbi, called/N_1344.contig-group-5.g.vcf.gz.tbi, called/N_1347.contig-group-5.g.vcf.gz.tbi, called/N_1354.contig-group-5.g.vcf.gz.tbi, called/N_1355.contig-group-5.g.vcf.gz.tbi, called/N_1384.contig-group-5.g.vcf.gz.tbi, called/N_1386.contig-group-5.g.vcf.gz.tbi, called/N_1390.contig-group-5.g.vcf.gz.tbi, called/N_1409.contig-group-5.g.vcf.gz.tbi, called/N_1411.contig-group-5.g.vcf.gz.tbi, called/N_1413.contig-group-5.g.vcf.gz.tbi, called/N_1414.contig-group-5.g.vcf.gz.tbi, called/N_1609.contig-group-5.g.vcf.gz.tbi, called/N_1870.contig-group-5.g.vcf.gz.tbi, called/N_1901.contig-group-5.g.vcf.gz.tbi, called/N_1913.contig-group-5.g.vcf.gz.tbi, called/N_1927.contig-group-5.g.vcf.gz.tbi, called/N_192.contig-group-5.g.vcf.gz.tbi, called/N_1934_1_1_368.contig-group-5.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-5.g.vcf.gz.tbi, called/N_1951_13_1951.contig-group-5.g.vcf.gz.tbi, called/N_1992_0123.contig-group-5.g.vcf.gz.tbi, called/N_1998_0130.contig-group-5.g.vcf.gz.tbi, called/N_2001_0025.contig-group-5.g.vcf.gz.tbi, called/N_2001_0205.contig-group-5.g.vcf.gz.tbi, called/N_2002_0292.contig-group-5.g.vcf.gz.tbi, called/N_2003_5409.contig-group-5.g.vcf.gz.tbi, called/N_2004.contig-group-5.g.vcf.gz.tbi, called/N_2010_1759.contig-group-5.g.vcf.gz.tbi, called/N_21.contig-group-5.g.vcf.gz.tbi, called/N_351.contig-group-5.g.vcf.gz.tbi, called/N_355.contig-group-5.g.vcf.gz.tbi, called/N_401.contig-group-5.g.vcf.gz.tbi, called/N_403.contig-group-5.g.vcf.gz.tbi, called/N_4843.contig-group-5.g.vcf.gz.tbi, called/N_4844.contig-group-5.g.vcf.gz.tbi, called/N_4846.contig-group-5.g.vcf.gz.tbi, called/N_4847.contig-group-5.g.vcf.gz.tbi, called/N_5056.contig-group-5.g.vcf.gz.tbi, called/N_5057.contig-group-5.g.vcf.gz.tbi, called/N_5129.contig-group-5.g.vcf.gz.tbi, called/N_6489.contig-group-5.g.vcf.gz.tbi, called/N_6490.contig-group-5.g.vcf.gz.tbi, called/N_685.contig-group-5.g.vcf.gz.tbi, called/N_689.contig-group-5.g.vcf.gz.tbi, called/N_690.contig-group-5.g.vcf.gz.tbi, called/N_6926.contig-group-5.g.vcf.gz.tbi, called/N_6928.contig-group-5.g.vcf.gz.tbi, called/N_6932.contig-group-5.g.vcf.gz.tbi, called/N_6.contig-group-5.g.vcf.gz.tbi, called/N_7083.contig-group-5.g.vcf.gz.tbi, called/N_79.contig-group-5.g.vcf.gz.tbi, called/N_7.contig-group-5.g.vcf.gz.tbi, called/N_8105.contig-group-5.g.vcf.gz.tbi, called/N_8171.contig-group-5.g.vcf.gz.tbi, called/N_83.contig-group-5.g.vcf.gz.tbi, called/N_8564.contig-group-5.g.vcf.gz.tbi, called/N_8565.contig-group-5.g.vcf.gz.tbi, called/N_8583.contig-group-5.g.vcf.gz.tbi, called/N_8585.contig-group-5.g.vcf.gz.tbi, called/N_8586.contig-group-5.g.vcf.gz.tbi, called/N_9104.contig-group-5.g.vcf.gz.tbi, called/N_9449.contig-group-5.g.vcf.gz.tbi, called/N_94.contig-group-5.g.vcf.gz.tbi, called/T1481.contig-group-5.g.vcf.gz.tbi, called/T1483.contig-group-5.g.vcf.gz.tbi, called/T178.contig-group-5.g.vcf.gz.tbi, called/T179.contig-group-5.g.vcf.gz.tbi, called/T180.contig-group-5.g.vcf.gz.tbi, called/T181.contig-group-5.g.vcf.gz.tbi, called/T185.contig-group-5.g.vcf.gz.tbi, called/T186.contig-group-5.g.vcf.gz.tbi, called/T187.contig-group-5.g.vcf.gz.tbi, called/T188.contig-group-5.g.vcf.gz.tbi, called/T189.contig-group-5.g.vcf.gz.tbi, called/T190.contig-group-5.g.vcf.gz.tbi, called/T192.contig-group-5.g.vcf.gz.tbi, called/T193.contig-group-5.g.vcf.gz.tbi, called/T194.contig-group-5.g.vcf.gz.tbi, called/T196.contig-group-5.g.vcf.gz.tbi, called/T248.contig-group-5.g.vcf.gz.tbi, called/T37.contig-group-5.g.vcf.gz.tbi, called/T72.contig-group-5.g.vcf.gz.tbi, called/T79.contig-group-5.g.vcf.gz.tbi output: called/all.contig-group-5.g.vcf.gz, called/all.contig-group-5.g.done log: logs/gatk/combine-gvcfs/contig-group-5.log jobid: 1885 benchmark: benchmarks/gatk/combine-gvcfs/contig-group-5.bench.log reason: Missing output files: called/all.contig-group-5.g.vcf.gz; Input files updated by another job: called/M5672.contig-group-5.g.vcf.gz, called/T180.contig-group-5.g.vcf.gz.tbi, called/N_8565.contig-group-5.g.vcf.gz, called/T192.contig-group-5.g.vcf.gz.tbi, called/N_8583.contig-group-5.g.vcf.gz, called/T1483.contig-group-5.g.vcf.gz, called/T187.contig-group-5.g.vcf.gz.tbi, called/N_5129.contig-group-5.g.vcf.gz, called/N_1156.contig-group-5.g.vcf.gz, called/T79.contig-group-5.g.vcf.gz.tbi, called/N_9104.contig-group-5.g.vcf.gz.tbi, called/N_6490.contig-group-5.g.vcf.gz.tbi, called/T196.contig-group-5.g.vcf.gz.tbi, called/N_1156.contig-group-5.g.vcf.gz.tbi, called/M5672.contig-group-5.g.vcf.gz.tbi, called/N_1354.contig-group-5.g.vcf.gz.tbi, called/N_83.contig-group-5.g.vcf.gz.tbi, called/N_6928.contig-group-5.g.vcf.gz.tbi, called/N_351.contig-group-5.g.vcf.gz.tbi, called/N_1870.contig-group-5.g.vcf.gz, called/N_9449.contig-group-5.g.vcf.gz.tbi, called/N_8171.contig-group-5.g.vcf.gz, called/T1483.contig-group-5.g.vcf.gz.tbi, called/T185.contig-group-5.g.vcf.gz, called/N_102.contig-group-5.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-5.g.vcf.gz.tbi, called/N_1354.contig-group-5.g.vcf.gz, called/N_690.contig-group-5.g.vcf.gz, called/N2005.contig-group-5.g.vcf.gz.tbi, called/N_1934_1_1_5973.contig-group-5.g.vcf.gz, called/N_8565.contig-group-5.g.vcf.gz.tbi, called/N_1609.contig-group-5.g.vcf.gz, called/T187.contig-group-5.g.vcf.gz, called/N_1870.contig-group-5.g.vcf.gz.tbi, called/T193.contig-group-5.g.vcf.gz, called/T190.contig-group-5.g.vcf.gz, called/T196.contig-group-5.g.vcf.gz, called/T79.contig-group-5.g.vcf.gz, called/N_4847.contig-group-5.g.vcf.gz.tbi, called/T192.contig-group-5.g.vcf.gz, called/N_8583.contig-group-5.g.vcf.gz.tbi, called/N_1158.contig-group-5.g.vcf.gz.tbi, called/N_1158.contig-group-5.g.vcf.gz, called/N_351.contig-group-5.g.vcf.gz, called/N_6928.contig-group-5.g.vcf.gz, called/N_6489.contig-group-5.g.vcf.gz, called/N_1609.contig-group-5.g.vcf.gz.tbi, called/T72.contig-group-5.g.vcf.gz.tbi, called/T193.contig-group-5.g.vcf.gz.tbi, called/N2005.contig-group-5.g.vcf.gz, called/T194.contig-group-5.g.vcf.gz, called/N_1992_0123.contig-group-5.g.vcf.gz.tbi, called/N_689.contig-group-5.g.vcf.gz, called/N_4843.contig-group-5.g.vcf.gz.tbi, called/N_1386.contig-group-5.g.vcf.gz, called/T72.contig-group-5.g.vcf.gz, called/N_102.contig-group-5.g.vcf.gz, called/N_2003_5409.contig-group-5.g.vcf.gz.tbi, called/T180.contig-group-5.g.vcf.gz, called/N_1927.contig-group-5.g.vcf.gz, called/N_79.contig-group-5.g.vcf.gz.tbi, called/N_1386.contig-group-5.g.vcf.gz.tbi, called/N_689.contig-group-5.g.vcf.gz.tbi, called/T190.contig-group-5.g.vcf.gz.tbi, called/N_1157.contig-group-5.g.vcf.gz, called/N_1157.contig-group-5.g.vcf.gz.tbi, called/N_4847.contig-group-5.g.vcf.gz, called/N_5129.contig-group-5.g.vcf.gz.tbi, called/N_8171.contig-group-5.g.vcf.gz.tbi, called/N_4843.contig-group-5.g.vcf.gz, called/N_6489.contig-group-5.g.vcf.gz.tbi, called/N_1992_0123.contig-group-5.g.vcf.gz, called/N_9104.contig-group-5.g.vcf.gz, called/T194.contig-group-5.g.vcf.gz.tbi, called/N_1927.contig-group-5.g.vcf.gz.tbi, called/N_690.contig-group-5.g.vcf.gz.tbi, called/N_79.contig-group-5.g.vcf.gz, called/N_83.contig-group-5.g.vcf.gz, called/T185.contig-group-5.g.vcf.gz.tbi, called/N_6490.contig-group-5.g.vcf.gz, called/N_2003_5409.contig-group-5.g.vcf.gz, called/N_9449.contig-group-5.g.vcf.gz wildcards: contig=contig-group-5 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-15.g.vcf.gz output: genotyped/all.contig-group-15.vcf.gz, genotyped/all.contig-group-15.done log: logs/gatk/genotype-gvcfs/contig-group-15.log jobid: 2844 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-15.bench.log reason: Input files updated by another job: called/all.contig-group-15.g.vcf.gz wildcards: contig=contig-group-15 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-8.g.vcf.gz output: genotyped/all.contig-group-8.vcf.gz, genotyped/all.contig-group-8.done log: logs/gatk/genotype-gvcfs/contig-group-8.log jobid: 2172 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-8.bench.log reason: Input files updated by another job: called/all.contig-group-8.g.vcf.gz wildcards: contig=contig-group-8 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-22.g.vcf.gz output: genotyped/all.contig-group-22.vcf.gz, genotyped/all.contig-group-22.done log: logs/gatk/genotype-gvcfs/contig-group-22.log jobid: 3516 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-22.bench.log reason: Input files updated by another job: called/all.contig-group-22.g.vcf.gz wildcards: contig=contig-group-22 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-1.g.vcf.gz output: genotyped/all.contig-group-1.vcf.gz, genotyped/all.contig-group-1.done log: logs/gatk/genotype-gvcfs/contig-group-1.log jobid: 1500 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-1.bench.log reason: Input files updated by another job: called/all.contig-group-1.g.vcf.gz wildcards: contig=contig-group-1 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-13.g.vcf.gz output: genotyped/all.contig-group-13.vcf.gz, genotyped/all.contig-group-13.done log: logs/gatk/genotype-gvcfs/contig-group-13.log jobid: 2652 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-13.bench.log reason: Input files updated by another job: called/all.contig-group-13.g.vcf.gz wildcards: contig=contig-group-13 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-6.g.vcf.gz output: genotyped/all.contig-group-6.vcf.gz, genotyped/all.contig-group-6.done log: logs/gatk/genotype-gvcfs/contig-group-6.log jobid: 1980 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-6.bench.log reason: Input files updated by another job: called/all.contig-group-6.g.vcf.gz wildcards: contig=contig-group-6 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-20.g.vcf.gz output: genotyped/all.contig-group-20.vcf.gz, genotyped/all.contig-group-20.done log: logs/gatk/genotype-gvcfs/contig-group-20.log jobid: 3324 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-20.bench.log reason: Input files updated by another job: called/all.contig-group-20.g.vcf.gz wildcards: contig=contig-group-20 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-4.g.vcf.gz output: genotyped/all.contig-group-4.vcf.gz, genotyped/all.contig-group-4.done log: logs/gatk/genotype-gvcfs/contig-group-4.log jobid: 1788 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-4.bench.log reason: Input files updated by another job: called/all.contig-group-4.g.vcf.gz wildcards: contig=contig-group-4 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-25.g.vcf.gz output: genotyped/all.contig-group-25.vcf.gz, genotyped/all.contig-group-25.done log: logs/gatk/genotype-gvcfs/contig-group-25.log jobid: 3804 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-25.bench.log reason: Input files updated by another job: called/all.contig-group-25.g.vcf.gz wildcards: contig=contig-group-25 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-0.g.vcf.gz output: genotyped/all.contig-group-0.vcf.gz, genotyped/all.contig-group-0.done log: logs/gatk/genotype-gvcfs/contig-group-0.log jobid: 1310 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-0.bench.log reason: Missing output files: genotyped/all.contig-group-0.vcf.gz; Input files updated by another job: called/all.contig-group-0.g.vcf.gz wildcards: contig=contig-group-0 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-11.g.vcf.gz output: genotyped/all.contig-group-11.vcf.gz, genotyped/all.contig-group-11.done log: logs/gatk/genotype-gvcfs/contig-group-11.log jobid: 2460 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-11.bench.log reason: Input files updated by another job: called/all.contig-group-11.g.vcf.gz wildcards: contig=contig-group-11 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-18.g.vcf.gz output: genotyped/all.contig-group-18.vcf.gz, genotyped/all.contig-group-18.done log: logs/gatk/genotype-gvcfs/contig-group-18.log jobid: 3132 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-18.bench.log reason: Input files updated by another job: called/all.contig-group-18.g.vcf.gz wildcards: contig=contig-group-18 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-16.g.vcf.gz output: genotyped/all.contig-group-16.vcf.gz, genotyped/all.contig-group-16.done log: logs/gatk/genotype-gvcfs/contig-group-16.log jobid: 2940 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-16.bench.log reason: Input files updated by another job: called/all.contig-group-16.g.vcf.gz wildcards: contig=contig-group-16 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-2.g.vcf.gz output: genotyped/all.contig-group-2.vcf.gz, genotyped/all.contig-group-2.done log: logs/gatk/genotype-gvcfs/contig-group-2.log jobid: 1596 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-2.bench.log reason: Missing output files: genotyped/all.contig-group-2.vcf.gz; Input files updated by another job: called/all.contig-group-2.g.vcf.gz wildcards: contig=contig-group-2 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-23.g.vcf.gz output: genotyped/all.contig-group-23.vcf.gz, genotyped/all.contig-group-23.done log: logs/gatk/genotype-gvcfs/contig-group-23.log jobid: 3612 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-23.bench.log reason: Input files updated by another job: called/all.contig-group-23.g.vcf.gz wildcards: contig=contig-group-23 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-9.g.vcf.gz output: genotyped/all.contig-group-9.vcf.gz, genotyped/all.contig-group-9.done log: logs/gatk/genotype-gvcfs/contig-group-9.log jobid: 2268 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-9.bench.log reason: Input files updated by another job: called/all.contig-group-9.g.vcf.gz wildcards: contig=contig-group-9 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-7.g.vcf.gz output: genotyped/all.contig-group-7.vcf.gz, genotyped/all.contig-group-7.done log: logs/gatk/genotype-gvcfs/contig-group-7.log jobid: 2076 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-7.bench.log reason: Input files updated by another job: called/all.contig-group-7.g.vcf.gz wildcards: contig=contig-group-7 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-21.g.vcf.gz output: genotyped/all.contig-group-21.vcf.gz, genotyped/all.contig-group-21.done log: logs/gatk/genotype-gvcfs/contig-group-21.log jobid: 3420 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-21.bench.log reason: Input files updated by another job: called/all.contig-group-21.g.vcf.gz wildcards: contig=contig-group-21 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-14.g.vcf.gz output: genotyped/all.contig-group-14.vcf.gz, genotyped/all.contig-group-14.done log: logs/gatk/genotype-gvcfs/contig-group-14.log jobid: 2748 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-14.bench.log reason: Input files updated by another job: called/all.contig-group-14.g.vcf.gz wildcards: contig=contig-group-14 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-26.g.vcf.gz output: genotyped/all.contig-group-26.vcf.gz, genotyped/all.contig-group-26.done log: logs/gatk/genotype-gvcfs/contig-group-26.log jobid: 3900 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-26.bench.log reason: Input files updated by another job: called/all.contig-group-26.g.vcf.gz wildcards: contig=contig-group-26 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-19.g.vcf.gz output: genotyped/all.contig-group-19.vcf.gz, genotyped/all.contig-group-19.done log: logs/gatk/genotype-gvcfs/contig-group-19.log jobid: 3228 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-19.bench.log reason: Input files updated by another job: called/all.contig-group-19.g.vcf.gz wildcards: contig=contig-group-19 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-12.g.vcf.gz output: genotyped/all.contig-group-12.vcf.gz, genotyped/all.contig-group-12.done log: logs/gatk/genotype-gvcfs/contig-group-12.log jobid: 2556 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-12.bench.log reason: Input files updated by another job: called/all.contig-group-12.g.vcf.gz wildcards: contig=contig-group-12 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-5.g.vcf.gz output: genotyped/all.contig-group-5.vcf.gz, genotyped/all.contig-group-5.done log: logs/gatk/genotype-gvcfs/contig-group-5.log jobid: 1884 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-5.bench.log reason: Missing output files: genotyped/all.contig-group-5.vcf.gz; Input files updated by another job: called/all.contig-group-5.g.vcf.gz wildcards: contig=contig-group-5 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-24.g.vcf.gz output: genotyped/all.contig-group-24.vcf.gz, genotyped/all.contig-group-24.done log: logs/gatk/genotype-gvcfs/contig-group-24.log jobid: 3708 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-24.bench.log reason: Input files updated by another job: called/all.contig-group-24.g.vcf.gz wildcards: contig=contig-group-24 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-3.g.vcf.gz output: genotyped/all.contig-group-3.vcf.gz, genotyped/all.contig-group-3.done log: logs/gatk/genotype-gvcfs/contig-group-3.log jobid: 1692 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-3.bench.log reason: Input files updated by another job: called/all.contig-group-3.g.vcf.gz wildcards: contig=contig-group-3 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-17.g.vcf.gz output: genotyped/all.contig-group-17.vcf.gz, genotyped/all.contig-group-17.done log: logs/gatk/genotype-gvcfs/contig-group-17.log jobid: 3036 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-17.bench.log reason: Input files updated by another job: called/all.contig-group-17.g.vcf.gz wildcards: contig=contig-group-17 [Mon Jul 29 13:38:43 2024] rule genotype_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.amb, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.ann, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.bwt, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.pac, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.sa, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict, called/all.contig-group-10.g.vcf.gz output: genotyped/all.contig-group-10.vcf.gz, genotyped/all.contig-group-10.done log: logs/gatk/genotype-gvcfs/contig-group-10.log jobid: 2364 benchmark: benchmarks/gatk/genotype-gvcfs/contig-group-10.bench.log reason: Input files updated by another job: called/all.contig-group-10.g.vcf.gz wildcards: contig=contig-group-10 [Mon Jul 29 13:38:43 2024] rule merge_variants: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.fai, genotyped/all.contig-group-0.vcf.gz, genotyped/all.contig-group-1.vcf.gz, genotyped/all.contig-group-2.vcf.gz, genotyped/all.contig-group-3.vcf.gz, genotyped/all.contig-group-4.vcf.gz, genotyped/all.contig-group-5.vcf.gz, genotyped/all.contig-group-6.vcf.gz, genotyped/all.contig-group-7.vcf.gz, genotyped/all.contig-group-8.vcf.gz, genotyped/all.contig-group-9.vcf.gz, genotyped/all.contig-group-10.vcf.gz, genotyped/all.contig-group-11.vcf.gz, genotyped/all.contig-group-12.vcf.gz, genotyped/all.contig-group-13.vcf.gz, genotyped/all.contig-group-14.vcf.gz, genotyped/all.contig-group-15.vcf.gz, genotyped/all.contig-group-16.vcf.gz, genotyped/all.contig-group-17.vcf.gz, genotyped/all.contig-group-18.vcf.gz, genotyped/all.contig-group-19.vcf.gz, genotyped/all.contig-group-20.vcf.gz, genotyped/all.contig-group-21.vcf.gz, genotyped/all.contig-group-22.vcf.gz, genotyped/all.contig-group-23.vcf.gz, genotyped/all.contig-group-24.vcf.gz, genotyped/all.contig-group-25.vcf.gz, genotyped/all.contig-group-26.vcf.gz output: genotyped/all.vcf.gz, genotyped/all.done log: logs/picard/merge-genotyped.log jobid: 1 benchmark: benchmarks/picard/merge-genotyped.bench.log reason: Missing output files: genotyped/all.vcf.gz; Input files updated by another job: genotyped/all.contig-group-8.vcf.gz, genotyped/all.contig-group-23.vcf.gz, genotyped/all.contig-group-9.vcf.gz, genotyped/all.contig-group-17.vcf.gz, genotyped/all.contig-group-22.vcf.gz, genotyped/all.contig-group-19.vcf.gz, genotyped/all.contig-group-4.vcf.gz, genotyped/all.contig-group-26.vcf.gz, genotyped/all.contig-group-11.vcf.gz, genotyped/all.contig-group-20.vcf.gz, genotyped/all.contig-group-15.vcf.gz, genotyped/all.contig-group-10.vcf.gz, genotyped/all.contig-group-18.vcf.gz, genotyped/all.contig-group-1.vcf.gz, genotyped/all.contig-group-5.vcf.gz, genotyped/all.contig-group-13.vcf.gz, genotyped/all.contig-group-24.vcf.gz, genotyped/all.contig-group-2.vcf.gz, genotyped/all.contig-group-16.vcf.gz, genotyped/all.contig-group-12.vcf.gz, genotyped/all.contig-group-21.vcf.gz, genotyped/all.contig-group-6.vcf.gz, genotyped/all.contig-group-7.vcf.gz, genotyped/all.contig-group-25.vcf.gz, genotyped/all.contig-group-14.vcf.gz, genotyped/all.contig-group-3.vcf.gz, genotyped/all.contig-group-0.vcf.gz [Mon Jul 29 13:38:43 2024] group job filtering (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule gatk_hard_filter_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, filtered/all.SNP.selected.vcf.gz, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict output: filtered/all.SNP.filtered.vcf.gz, filtered/all.SNP.filtered.done log: logs/gatk/variantfiltration/SNP.log jobid: 4 benchmark: benchmarks/gatk/variantfiltration/SNP.bench.log reason: Missing output files: filtered/all.SNP.filtered.vcf.gz; Input files updated by another job: filtered/all.SNP.selected.vcf.gz wildcards: vartype=SNP [Mon Jul 29 13:38:43 2024] rule select_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, genotyped/all.vcf.gz, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict output: filtered/all.SNP.selected.vcf.gz, filtered/all.SNP.selected.done log: logs/gatk/selectvariants/SNP.log jobid: 5 benchmark: benchmarks/gatk/selectvariants/SNP.bench.log reason: Missing output files: filtered/all.SNP.selected.vcf.gz; Input files updated by another job: genotyped/all.vcf.gz wildcards: vartype=SNP [Mon Jul 29 13:38:43 2024] group job filtering (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule gatk_hard_filter_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, filtered/all.INDEL.selected.vcf.gz, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict output: filtered/all.INDEL.filtered.vcf.gz, filtered/all.INDEL.filtered.done log: logs/gatk/variantfiltration/INDEL.log jobid: 7 benchmark: benchmarks/gatk/variantfiltration/INDEL.bench.log reason: Missing output files: filtered/all.INDEL.filtered.vcf.gz; Input files updated by another job: filtered/all.INDEL.selected.vcf.gz wildcards: vartype=INDEL [Mon Jul 29 13:38:43 2024] rule select_calls: input: /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta, genotyped/all.vcf.gz, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.dict output: filtered/all.INDEL.selected.vcf.gz, filtered/all.INDEL.selected.done log: logs/gatk/selectvariants/INDEL.log jobid: 8 benchmark: benchmarks/gatk/selectvariants/INDEL.bench.log reason: Missing output files: filtered/all.INDEL.selected.vcf.gz; Input files updated by another job: genotyped/all.vcf.gz wildcards: vartype=INDEL [Mon Jul 29 13:38:43 2024] rule merge_calls: input: filtered/all.SNP.filtered.vcf.gz, filtered/all.INDEL.filtered.vcf.gz output: filtered/all.vcf.gz, filtered/all.done log: logs/picard/merge-filtered.log jobid: 3 benchmark: benchmarks/picard/merge-filtered.bench.log reason: Missing output files: filtered/all.vcf.gz; Input files updated by another job: filtered/all.SNP.filtered.vcf.gz, filtered/all.INDEL.filtered.vcf.gz [Mon Jul 29 13:38:43 2024] group job bcftools-stats (jobs in lexicogr. order): [Mon Jul 29 13:38:43 2024] rule bcftools_stats: input: filtered/all.vcf.gz output: qc/bcftools-stats/stats.vchk log: logs/bcftools-stats/bcftools.stats.log jobid: 1160 reason: Missing output files: qc/bcftools-stats/stats.vchk; Input files updated by another job: filtered/all.vcf.gz [Mon Jul 29 13:38:43 2024] rule bcftools_stats_plot: input: qc/bcftools-stats/stats.vchk output: qc/bcftools-stats/summary.pdf log: logs/bcftools-stats/bcftools.stats.plot.log jobid: 1161 reason: Missing output files: qc/bcftools-stats/summary.pdf; Input files updated by another job: qc/bcftools-stats/stats.vchk ( plot-vcfstats --prefix qc/bcftools-stats qc/bcftools-stats/stats.vchk &> logs/bcftools-stats/bcftools.stats.plot.log || true ) ; if [ -f qc/bcftools-stats/summary.pdf ]; then echo "Success with pdflatex" >> logs/bcftools-stats/bcftools.stats.plot.log ; else echo "Failed with pdflatex" >> logs/bcftools-stats/bcftools.stats.plot.log ; echo "Trying tectonic instead" >> logs/bcftools-stats/bcftools.stats.plot.log ; tectonic qc/bcftools-stats/summary.tex >> logs/bcftools-stats/bcftools.stats.plot.log 2>&1 ; fi [Mon Jul 29 13:38:43 2024] rule multiqc: input: qc/fastqc/fastqc.done, trimmed/trimming-reports.done, qc/samtools-stats/samtools-stats.done, qc/samtools-flagstat/samtools-flagstat.done, qc/qualimap/qualimap.done, qc/picard/collectmultiplemetrics.done, qc/dedup/picard.done, qc/bcftools-stats/stats.vchk, qc/bcftools-stats/summary.pdf output: qc/multiqc.html log: logs/multiqc.log jobid: 9 reason: Missing output files: qc/multiqc.html; Input files updated by another job: qc/bcftools-stats/summary.pdf, qc/bcftools-stats/stats.vchk [Mon Jul 29 13:38:43 2024] localrule all: input: genotyped/all.vcf.gz, filtered/all.vcf.gz, qc/multiqc.html, /dss/dsslegfs01/pr53da/pr53da-dss-0026/assemblies/Poecile_montanus_v1.0_12.07.2024/12.07.24_Poecile.montanus__genome.mitogenome__N2005.N2008__PacBioHiFi.Hi-C.Illumina__hifiasm.yahs.ragtag.mitofinder__v1.0.fasta.seqkit jobid: 0 reason: Input files updated by another job: qc/multiqc.html, genotyped/all.vcf.gz, filtered/all.vcf.gz Job counts: count jobs 1 all 39 bam_index 1 bcftools_stats 1 bcftools_stats_plot 1057 call_variants 27 combine_calls 2 gatk_hard_filter_calls 27 genotype_variants 1 merge_calls 1 merge_variants 1 multiqc 2 select_calls 1160 This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.