Building DAG of jobs... Using shell: /bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Provided resources: mem_mb=64000 Conda environments: ignored Job counts: count jobs 1 LongOrfs 1 Predict 1 all 24 assemble_transcripts_fq 1 base_recalibration 1 blastp 1 call_gvcf_varaints 1 call_vcf_variants 1 cdna_alignment_orf_to_genome_orf 1 copy_gff3_to_snpeff 1 custom_protein_xml 1 final_vcf_naming 1 finish_isoform 1 finish_isoform_variants 1 finish_variants 1 generate_snpeff_database 1 gtf_file_to_cDNA_seqs 1 gtf_to_alignment_gff3 21 hisat2_align_bam_fq 1 hisat2_groupmark_bam 1 hisat2_merge_bams 1 merge_transcripts 1 reference_protein_xml 1 remove_exon_and_utr_information 1 split_n_cigar_reads 1 transfer_modifications_isoformvariant 1 transfer_modifications_variant 1 variant_annotation_custom 1 variant_annotation_ref 72 [Wed Apr 7 14:58:58 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 18 wildcards: dir=/home/animeshs/rnAGS, fq=22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 14:58:58 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 40 wildcards: dir=/home/animeshs/rnAGS, fq=22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 15:44:29 2021] Finished job 40. 1 of 72 steps (1%) done [Wed Apr 7 15:44:29 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 98 wildcards: dir=/home/animeshs/rnAGS, fq=22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 15:44:29 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 106 wildcards: dir=/home/animeshs/rnAGS, fq=22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 15:48:18 2021] Finished job 98. 2 of 72 steps (3%) done [Wed Apr 7 15:48:47 2021] Finished job 18. 3 of 72 steps (4%) done [Wed Apr 7 15:48:47 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 93 wildcards: dir=/home/animeshs/rnAGS, fq=22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 15:48:47 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 84 wildcards: dir=/home/animeshs/rnAGS, fq=22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 15:48:47 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 83 wildcards: dir=/home/animeshs/rnAGS, fq=22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 15:50:38 2021] Finished job 106. 4 of 72 steps (6%) done [Wed Apr 7 15:54:39 2021] Finished job 93. 5 of 72 steps (7%) done [Wed Apr 7 15:55:31 2021] Finished job 83. 6 of 72 steps (8%) done [Wed Apr 7 15:56:37 2021] Finished job 84. 7 of 72 steps (10%) done [Wed Apr 7 15:56:37 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 44 wildcards: dir=/home/animeshs/rnAGS, fq=22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 15:56:37 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 48 wildcards: dir=/home/animeshs/rnAGS, fq=22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 16:45:25 2021] Finished job 48. 8 of 72 steps (11%) done [Wed Apr 7 16:45:25 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 32 wildcards: dir=/home/animeshs/rnAGS, fq=22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 16:59:22 2021] Finished job 44. 9 of 72 steps (12%) done [Wed Apr 7 16:59:22 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 60 wildcards: dir=/home/animeshs/rnAGS, fq=22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 17:27:01 2021] Finished job 32. 10 of 72 steps (14%) done [Wed Apr 7 17:27:01 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 95 wildcards: dir=/home/animeshs/rnAGS, fq=22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 17:27:01 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 89 wildcards: dir=/home/animeshs/rnAGS, fq=22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 17:32:14 2021] Finished job 89. 11 of 72 steps (15%) done [Wed Apr 7 17:34:06 2021] Finished job 95. 12 of 72 steps (17%) done [Wed Apr 7 17:40:10 2021] Finished job 60. 13 of 72 steps (18%) done [Wed Apr 7 17:40:10 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 30 wildcards: dir=/home/animeshs/rnAGS, fq=22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 17:40:10 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 46 wildcards: dir=/home/animeshs/rnAGS, fq=22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 18:24:12 2021] Finished job 46. 14 of 72 steps (19%) done [Wed Apr 7 18:24:13 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 96 wildcards: dir=/home/animeshs/rnAGS, fq=22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 18:24:13 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 103 wildcards: dir=/home/animeshs/rnAGS, fq=22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 18:29:33 2021] Finished job 96. 15 of 72 steps (21%) done [Wed Apr 7 18:30:10 2021] Finished job 103. 16 of 72 steps (22%) done [Wed Apr 7 18:33:38 2021] Finished job 30. 17 of 72 steps (24%) done [Wed Apr 7 18:33:38 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 64 wildcards: dir=/home/animeshs/rnAGS, fq=22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 18:33:38 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 42 wildcards: dir=/home/animeshs/rnAGS, fq=22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 19:14:14 2021] Finished job 64. 18 of 72 steps (25%) done [Wed Apr 7 19:14:14 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 52 wildcards: dir=/home/animeshs/rnAGS, fq=22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 19:16:10 2021] Finished job 42. 19 of 72 steps (26%) done [Wed Apr 7 19:16:11 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 94 wildcards: dir=/home/animeshs/rnAGS, fq=22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 19:16:11 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 97 wildcards: dir=/home/animeshs/rnAGS, fq=22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 19:26:28 2021] Finished job 94. 20 of 72 steps (28%) done [Wed Apr 7 19:28:25 2021] Finished job 97. 21 of 72 steps (29%) done [Wed Apr 7 19:50:03 2021] Finished job 52. 22 of 72 steps (31%) done [Wed Apr 7 19:50:04 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 56 wildcards: dir=/home/animeshs/rnAGS, fq=22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 19:50:04 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 62 wildcards: dir=/home/animeshs/rnAGS, fq=22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 20:35:10 2021] Finished job 62. 23 of 72 steps (32%) done [Wed Apr 7 20:35:11 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 28 wildcards: dir=/home/animeshs/rnAGS, fq=22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 20:53:09 2021] Finished job 56. 24 of 72 steps (33%) done [Wed Apr 7 20:53:09 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 99 wildcards: dir=/home/animeshs/rnAGS, fq=22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 20:53:09 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 88 wildcards: dir=/home/animeshs/rnAGS, fq=22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 21:00:56 2021] Finished job 99. 25 of 72 steps (35%) done [Wed Apr 7 21:03:40 2021] Finished job 88. 26 of 72 steps (36%) done [Wed Apr 7 21:23:49 2021] Finished job 28. 27 of 72 steps (38%) done [Wed Apr 7 21:23:49 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 101 wildcards: dir=/home/animeshs/rnAGS, fq=22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 21:23:50 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 104 wildcards: dir=/home/animeshs/rnAGS, fq=22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 21:23:50 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 87 wildcards: dir=/home/animeshs/rnAGS, fq=22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 21:23:50 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 105 wildcards: dir=/home/animeshs/rnAGS, fq=22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 21:30:03 2021] Finished job 104. 28 of 72 steps (39%) done [Wed Apr 7 21:30:43 2021] Finished job 105. 29 of 72 steps (40%) done [Wed Apr 7 21:31:29 2021] Finished job 87. 30 of 72 steps (42%) done [Wed Apr 7 21:31:34 2021] Finished job 101. 31 of 72 steps (43%) done [Wed Apr 7 21:31:34 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 26 wildcards: dir=/home/animeshs/rnAGS, fq=22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 21:31:34 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 58 wildcards: dir=/home/animeshs/rnAGS, fq=22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 22:14:00 2021] Finished job 26. 32 of 72 steps (44%) done [Wed Apr 7 22:14:00 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 24 wildcards: dir=/home/animeshs/rnAGS, fq=22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 22:17:14 2021] Finished job 58. 33 of 72 steps (46%) done [Wed Apr 7 22:17:14 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 36 wildcards: dir=/home/animeshs/rnAGS, fq=22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 22:52:03 2021] Finished job 24. 34 of 72 steps (47%) done [Wed Apr 7 22:52:03 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 102 wildcards: dir=/home/animeshs/rnAGS, fq=22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 22:52:03 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 86 wildcards: dir=/home/animeshs/rnAGS, fq=22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 22:55:58 2021] Finished job 36. 35 of 72 steps (49%) done [Wed Apr 7 22:55:58 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 85 wildcards: dir=/home/animeshs/rnAGS, fq=22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Wed Apr 7 22:55:58 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 91 wildcards: dir=/home/animeshs/rnAGS, fq=22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Wed Apr 7 22:57:40 2021] Finished job 86. 36 of 72 steps (50%) done [Wed Apr 7 22:58:14 2021] Finished job 102. 37 of 72 steps (51%) done [Wed Apr 7 23:00:59 2021] Finished job 85. 38 of 72 steps (53%) done [Wed Apr 7 23:01:12 2021] Finished job 91. 39 of 72 steps (54%) done [Wed Apr 7 23:01:12 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.hisat2.log jobid: 54 wildcards: dir=/home/animeshs/rnAGS, fq=22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam. threads: 12 [Wed Apr 7 23:01:12 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.hisat2.log jobid: 34 wildcards: dir=/home/animeshs/rnAGS, fq=22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam. threads: 12 [Wed Apr 7 23:44:47 2021] Finished job 34. 40 of 72 steps (56%) done [Wed Apr 7 23:44:47 2021] rule hisat2_align_bam_fq: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.1.ht2, /home/animeshs/rnAGS/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_1.fastq.gz, /home/animeshs/rnAGS/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.trim_2.fastq.gz, data/ensembl/Homo_sapiens.GRCh38.97.splicesites.txt output: /home/animeshs/rnAGS/align/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam log: /home/animeshs/rnAGS/align/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.hisat2.log jobid: 38 wildcards: dir=/home/animeshs/rnAGS, fq=22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam. threads: 12 [Wed Apr 7 23:52:25 2021] Finished job 54. 41 of 72 steps (57%) done [Wed Apr 7 23:52:25 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 100 wildcards: dir=/home/animeshs/rnAGS, fq=22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam. threads: 6 [Wed Apr 7 23:52:25 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 90 wildcards: dir=/home/animeshs/rnAGS, fq=22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam. threads: 6 [Thu Apr 8 00:02:20 2021] Finished job 90. 42 of 72 steps (58%) done [Thu Apr 8 00:03:50 2021] Finished job 100. 43 of 72 steps (60%) done [Thu Apr 8 00:32:37 2021] Finished job 38. 44 of 72 steps (61%) done [Thu Apr 8 00:32:37 2021] rule assemble_transcripts_fq: input: /home/animeshs/rnAGS/align/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf log: /home/animeshs/rnAGS/isoforms/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf.log jobid: 92 wildcards: dir=/home/animeshs/rnAGS, fq=22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam. threads: 6 [Thu Apr 8 00:32:37 2021] rule hisat2_merge_bams: input: /home/animeshs/rnAGS/align/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam, /home/animeshs/rnAGS/align/22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.bam output: /home/animeshs/rnAGS/align/combined.sorted.bam, /home/animeshs/rnAGS/align/combined.sorted.stats log: /home/animeshs/rnAGS/align/combined.sorted.log jobid: 17 wildcards: dir=/home/animeshs/rnAGS threads: 12 resources: mem_mb=16000 [Thu Apr 8 00:32:37 2021] rule reference_protein_xml: input: SnpEff/data/Homo_sapiens.GRCh38/doneHomo_sapiens.GRCh38.txt, SnpEff/snpEff.jar, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll, data/uniprot/Homo_sapiens.protein.xml.gz output: /home/animeshs/rnAGS/variants/doneHomo_sapiens.GRCh38.97.txt, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml.gz, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.fasta, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withdecoys.fasta, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml.gz log: /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.spritz.log jobid: 74 benchmark: /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.spritz.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 [Thu Apr 8 00:34:56 2021] Error in rule reference_protein_xml: jobid: 74 output: /home/animeshs/rnAGS/variants/doneHomo_sapiens.GRCh38.97.txt, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml.gz, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.fasta, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withdecoys.fasta, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml, /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml.gz log: /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.spritz.log (check log file(s) for error message) shell: (java -Xmx16000M -jar SnpEff/snpEff.jar -v -nostats -xmlProt /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml Homo_sapiens.GRCh38 && dotnet TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll -x data/uniprot/Homo_sapiens.protein.xml.gz -y /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml && gzip -k /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.withmods.xml /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml) &> /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.spritz.log && touch /home/animeshs/rnAGS/variants/doneHomo_sapiens.GRCh38.97.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Removing output files of failed job reference_protein_xml since they might be corrupted: /home/animeshs/rnAGS/variants/Homo_sapiens.GRCh38.97.protein.xml Job failed, going on with independent jobs. [Thu Apr 8 00:41:01 2021] Finished job 92. 45 of 72 steps (62%) done [Thu Apr 8 00:41:01 2021] rule merge_transcripts: input: /home/animeshs/rnAGS/isoforms/22286_CGATGT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22287_TGACCA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22288_ACAGTG_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22290_CAGATC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22291_CTTGTA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22292_AGTCAA_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22293_AGTTCC_C5E7AANXX_5_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22294_ATGTCA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22295_CCGTCC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22296_GTCCGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22297_GTGAAA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22298_ATCACG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22299_TTAGGC_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22300_ACTTGA_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22301_GATCAG_C5E7AANXX_6_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22302_TAGCTT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22303_GGCTAC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22304_GTGGCC_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22305_GTTTCG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22306_CGTACG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22307_GAGTGG_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, /home/animeshs/rnAGS/isoforms/22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam..fq.sorted.gtf, data/ensembl/Homo_sapiens.GRCh38.97.gff3 output: /home/animeshs/rnAGS/isoforms/combined.gtf log: /home/animeshs/rnAGS/isoforms/combined.gtf.log jobid: 82 benchmark: /home/animeshs/rnAGS/isoforms/combined.gtf.benchmark wildcards: dir=/home/animeshs/rnAGS threads: 12 [Thu Apr 8 00:50:32 2021] Finished job 82. 46 of 72 steps (64%) done [Thu Apr 8 00:50:32 2021] rule gtf_file_to_cDNA_seqs: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa, /home/animeshs/rnAGS/isoforms/combined.gtf output: /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta, /home/animeshs/rnAGS/isoforms/combined.transcripts.gtf log: /home/animeshs/rnAGS/isoforms/combined.gtf_file_to_cDNA_seqs.log jobid: 81 benchmark: /home/animeshs/rnAGS/isoforms/combined.gtf_file_to_cDNA_seqs.benchmark wildcards: dir=/home/animeshs/rnAGS [Thu Apr 8 00:51:14 2021] Finished job 81. 47 of 72 steps (65%) done [Thu Apr 8 00:51:14 2021] rule gtf_to_alignment_gff3: input: /home/animeshs/rnAGS/isoforms/combined.transcripts.gtf output: /home/animeshs/rnAGS/isoforms/combined.transcripts.gff3 log: /home/animeshs/rnAGS/isoforms/combined.gtf_to_alignment_gff3.log jobid: 80 benchmark: /home/animeshs/rnAGS/isoforms/combined.gtf_to_alignment_gff3.benchmark wildcards: dir=/home/animeshs/rnAGS [Thu Apr 8 00:51:14 2021] rule LongOrfs: input: /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta output: /home/animeshs/rnAGS/isoforms/longest_orfs.pep, /home/animeshs/rnAGS/isoforms.__checkpoints_longorfs log: /home/animeshs/rnAGS/isoforms/combined.LongOrfs.log jobid: 108 benchmark: /home/animeshs/rnAGS/isoforms/combined.LongOrfs.benchmark wildcards: dir=/home/animeshs/rnAGS [Thu Apr 8 00:51:34 2021] Finished job 80. 48 of 72 steps (67%) done [Thu Apr 8 00:58:47 2021] Finished job 108. 49 of 72 steps (68%) done [Thu Apr 8 07:11:37 2021] Finished job 17. 50 of 72 steps (69%) done [Thu Apr 8 07:11:37 2021] rule hisat2_groupmark_bam: input: /home/animeshs/rnAGS/align/combined.sorted.bam, tmp output: /home/animeshs/rnAGS/variants/combined.sorted.grouped.bam, /home/animeshs/rnAGS/variants/combined.sorted.grouped.bam.bai, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.bam, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.bam.bai, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.metrics log: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.log jobid: 16 benchmark: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 [Thu Apr 8 07:11:38 2021] rule blastp: input: data/uniprot/Homo_sapiens.protein.fasta, /home/animeshs/rnAGS/isoforms/longest_orfs.pep, data/uniprot/Homo_sapiens.protein.fasta.pin, data/uniprot/Homo_sapiens.protein.fasta.phr, data/uniprot/Homo_sapiens.protein.fasta.psq output: /home/animeshs/rnAGS/isoforms/combined.blastp.outfmt6 log: /home/animeshs/rnAGS/isoforms/combined.blastp.log jobid: 109 benchmark: /home/animeshs/rnAGS/isoforms/combined.blastp.benchmark wildcards: dir=/home/animeshs/rnAGS threads: 23 [Thu Apr 8 10:26:51 2021] Finished job 109. 51 of 72 steps (71%) done [Thu Apr 8 10:26:52 2021] rule Predict: input: /home/animeshs/rnAGS/isoforms/longest_orfs.pep, /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta, /home/animeshs/rnAGS/isoforms/combined.blastp.outfmt6, /home/animeshs/rnAGS/isoforms.__checkpoints_longorfs output: /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta.transdecoder.pep, /home/animeshs/rnAGS/isoforms/..__checkpoints, /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta.transdecoder.gff3 log: /home/animeshs/rnAGS/isoforms/combined.Predict.log jobid: 107 benchmark: /home/animeshs/rnAGS/isoforms/combined.Predict.benchmark wildcards: dir=/home/animeshs/rnAGS /bin/bash: ../..//home/animeshs/rnAGS/isoforms/combined.Predict.log: No such file or directory [Thu Apr 8 10:26:52 2021] Error in rule Predict: jobid: 107 output: /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta.transdecoder.pep, /home/animeshs/rnAGS/isoforms/..__checkpoints, /home/animeshs/rnAGS/isoforms/combined.transcripts.fasta.transdecoder.gff3 log: /home/animeshs/rnAGS/isoforms/combined.Predict.log (check log file(s) for error message) shell: cd /home/animeshs/rnAGS/isoforms && TransDecoder.Predict -O . -t ../..//home/animeshs/rnAGS/isoforms/combined.transcripts.fasta --single_best_only --retain_blastp_hits ../..//home/animeshs/rnAGS/isoforms/combined.blastp.outfmt6 2> ../..//home/animeshs/rnAGS/isoforms/combined.Predict.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Job failed, going on with independent jobs. Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.bam. Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.bam.bai. [Fri Apr 9 06:03:39 2021] Finished job 16. 52 of 72 steps (72%) done [Fri Apr 9 06:03:39 2021] rule split_n_cigar_reads: input: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.bam, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa.fai, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.dict, tmp output: /home/animeshs/rnAGS/variants/combined.fixedQuals.bam, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.bam, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.bam.bai log: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.log jobid: 15 benchmark: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 Removing temporary output file /home/animeshs/rnAGS/variants/combined.fixedQuals.bam. Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.bam.bai. [Sun Apr 11 15:29:14 2021] Finished job 15. 53 of 72 steps (74%) done [Sun Apr 11 15:29:15 2021] rule base_recalibration: input: data/ensembl/Homo_sapiens.ensembl.vcf, data/ensembl/Homo_sapiens.ensembl.vcf.idx, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.bam, tmp output: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recaltable, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.bam log: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.log jobid: 14 benchmark: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.bam. Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recaltable. [Mon Apr 12 02:00:37 2021] Finished job 14. 54 of 72 steps (75%) done [Mon Apr 12 02:00:37 2021] rule call_gvcf_varaints: input: data/ensembl/Homo_sapiens.ensembl.vcf, data/ensembl/Homo_sapiens.ensembl.vcf.idx, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.bam, tmp output: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.vcf.gz log: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.log jobid: 10 benchmark: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.benchmark wildcards: dir=/home/animeshs/rnAGS threads: 8 resources: mem_mb=16000 Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.bam. [Mon Apr 12 18:57:04 2021] Finished job 10. 55 of 72 steps (76%) done [Mon Apr 12 18:57:04 2021] rule call_vcf_variants: input: data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.vcf.gz, tmp output: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.gt.vcf log: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.gt.log jobid: 9 benchmark: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.gt.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 Removing temporary output file /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.vcf.gz. Removing temporary output file tmp. [Mon Apr 12 19:08:42 2021] Finished job 9. 56 of 72 steps (78%) done [Mon Apr 12 19:08:42 2021] rule final_vcf_naming: input: /home/animeshs/rnAGS/variants/combined.sorted.grouped.marked.split.recal.g.gt.vcf output: /home/animeshs/rnAGS/variants/combined.spritz.vcf log: /home/animeshs/rnAGS/variants/final_vcf_naming.log jobid: 8 wildcards: dir=/home/animeshs/rnAGS [Mon Apr 12 19:08:42 2021] Finished job 8. 57 of 72 steps (79%) done [Mon Apr 12 19:08:42 2021] rule variant_annotation_ref: input: SnpEff/data/Homo_sapiens.GRCh38/doneHomo_sapiens.GRCh38.txt, SnpEff/snpEff.jar, data/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.karyotypic.fa, /home/animeshs/rnAGS/variants/combined.spritz.vcf output: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.vcf, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.html, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.genes.txt, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.fasta, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml log: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.log jobid: 3 benchmark: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.benchmark wildcards: dir=/home/animeshs/rnAGS resources: mem_mb=16000 [Mon Apr 12 19:19:29 2021] Finished job 3. 58 of 72 steps (81%) done [Mon Apr 12 19:19:30 2021] rule transfer_modifications_variant: input: TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll, data/uniprot/Homo_sapiens.protein.xml.gz, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml output: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withdecoys.fasta, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml.gz, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.xml, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.xml.gz log: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.log jobid: 71 benchmark: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.benchmark wildcards: dir=/home/animeshs/rnAGS [Mon Apr 12 19:19:30 2021] Error in rule transfer_modifications_variant: jobid: 71 output: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withdecoys.fasta, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml.gz, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.xml, /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.xml.gz log: /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.log (check log file(s) for error message) shell: (dotnet TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll -x data/uniprot/Homo_sapiens.protein.xml.gz -y /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml && gzip -k /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.xml /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.xml) &> /home/animeshs/rnAGS/variants/combined.spritz.snpeff.protein.withmods.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Job failed, going on with independent jobs. Exiting because a job execution failed. Look above for error message Complete log: /home/animeshs/Spritz/Spritz/.snakemake/log/2021-04-07T145856.459379.snakemake.log