Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 1000
Job stats:
job                        count    min threads    max threads
-----------------------  -------  -------------  -------------
DB2vcf                       270              1              1
all                            1              1              1
callable_bed                   1              1              1
collect_covstats               1              1              1
compute_d4                     9              4              4
concat_gvcfs                   9              1              1
create_cov_bed                 1              1              1
create_db_mapfile              1              1              1
create_gvcf_intervals          1              1              1
filterVcfs                   270              1              1
gvcf2DB                      270              1              1
merge_d4                       1              1              1
qc_admixture                   1              1              1
qc_check_fai                   1              1              1
qc_plink                       1              1              1
qc_qc_plots                    1              1              1
qc_subsample_snps              1              1              1
qc_vcftools_individuals        1              1              1
sort_gatherVcfs                1              1              1
total                        842              1              4

Select jobs to execute...

[Mon Aug  7 14:06:19 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    jobid: 58
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=8218, disk_mib=7838, tmpdir=<TBD>

Submitted job 58 with external jobid '65586840'.

[Mon Aug  7 14:06:21 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    jobid: 60
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=9187, disk_mib=8762, tmpdir=<TBD>

Submitted job 60 with external jobid '65586841'.

[Mon Aug  7 14:06:22 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    jobid: 63
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A07v1_coca_846_S58_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=1716, disk_mib=1637, tmpdir=<TBD>

Submitted job 63 with external jobid '65586842'.

[Mon Aug  7 14:06:23 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    jobid: 62
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A06v1_grac_794_S50_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=6400, disk_mib=6104, tmpdir=<TBD>

Submitted job 62 with external jobid '65586843'.

[Mon Aug  7 14:06:24 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    jobid: 57
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_864_S1_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=3368, disk_mib=3212, tmpdir=<TBD>

Submitted job 57 with external jobid '65586844'.

[Mon Aug  7 14:06:27 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    jobid: 59
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A03v1_grac_868_S26_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=4096, disk_mib=3907, tmpdir=<TBD>

Submitted job 59 with external jobid '65586856'.

[Mon Aug  7 14:06:28 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    jobid: 61
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=5317, disk_mib=5071, tmpdir=<TBD>

Submitted job 61 with external jobid '65586857'.

[Mon Aug  7 14:06:29 2023]
checkpoint create_gvcf_intervals:
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt
    jobid: 79
    benchmark: benchmarks/GCA_026413385.1/gvcf_intervals/benchmark.txt
    reason: Missing output files: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
    wildcards: refGenome=GCA_026413385.1
    resources: mem_mb=1197, mem_mib=1142, disk_mb=1197, disk_mib=1142, tmpdir=<TBD>
DAG of jobs will be updated after completion.

Submitted job 79 with external jobid '65586858'.

[Mon Aug  7 14:06:31 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    jobid: 64
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A08v1_novo_777_S66_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=5604, disk_mib=5345, tmpdir=<TBD>

Submitted job 64 with external jobid '65586859'.

[Mon Aug  7 14:06:32 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    jobid: 56
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_815_S10_L004
    threads: 4
    resources: mem_mb=4000, mem_mib=3815, disk_mb=7473, disk_mib=7127, tmpdir=<TBD>

Submitted job 56 with external jobid '65586860'.
[Mon Aug  7 14:06:55 2023]
Error in rule compute_d4:
    jobid: 58
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586840

Error executing rule compute_d4 on cluster (jobid: 58, external: 65586840, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.58.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 58.
Select jobs to execute...

[Mon Aug  7 14:06:55 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    jobid: 58
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=8218, disk_mib=7838, tmpdir=<TBD>

[Mon Aug  7 14:06:56 2023]
Error in rule compute_d4:
    jobid: 60
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586841

Error executing rule compute_d4 on cluster (jobid: 60, external: 65586841, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.60.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:06:56 2023]
Error in rule compute_d4:
    jobid: 63
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586842

Error executing rule compute_d4 on cluster (jobid: 63, external: 65586842, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.63.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:06:56 2023]
Error in rule compute_d4:
    jobid: 62
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586843

Error executing rule compute_d4 on cluster (jobid: 62, external: 65586843, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.62.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 58 with external jobid '65586873'.
Trying to restart job 60.
Trying to restart job 63.
Trying to restart job 62.
Select jobs to execute...

[Mon Aug  7 14:06:59 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    jobid: 63
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A07v1_coca_846_S58_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=1716, disk_mib=1637, tmpdir=<TBD>

Submitted job 63 with external jobid '65586874'.

[Mon Aug  7 14:07:01 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    jobid: 62
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A06v1_grac_794_S50_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=6400, disk_mib=6104, tmpdir=<TBD>

Submitted job 62 with external jobid '65586875'.

[Mon Aug  7 14:07:03 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    jobid: 60
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=9187, disk_mib=8762, tmpdir=<TBD>

Submitted job 60 with external jobid '65586876'.
[Mon Aug  7 14:07:21 2023]
Error in rule compute_d4:
    jobid: 61
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586857

Error executing rule compute_d4 on cluster (jobid: 61, external: 65586857, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.61.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 61.
Select jobs to execute...

[Mon Aug  7 14:07:21 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    jobid: 61
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=5317, disk_mib=5071, tmpdir=<TBD>

[Mon Aug  7 14:07:22 2023]
Error in rule compute_d4:
    jobid: 57
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586844

Error executing rule compute_d4 on cluster (jobid: 57, external: 65586844, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.57.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:07:22 2023]
Error in rule compute_d4:
    jobid: 59
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586856

Error executing rule compute_d4 on cluster (jobid: 59, external: 65586856, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.59.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:07:23 2023]
Error in rule compute_d4:
    jobid: 64
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586859

Error executing rule compute_d4 on cluster (jobid: 64, external: 65586859, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.64.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 61 with external jobid '65586881'.
Trying to restart job 57.
Trying to restart job 59.
Trying to restart job 64.
Select jobs to execute...

[Mon Aug  7 14:07:23 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    jobid: 57
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_864_S1_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=3368, disk_mib=3212, tmpdir=<TBD>

Submitted job 57 with external jobid '65586882'.

[Mon Aug  7 14:07:24 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    jobid: 64
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A08v1_novo_777_S66_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=5604, disk_mib=5345, tmpdir=<TBD>

Submitted job 64 with external jobid '65586883'.

[Mon Aug  7 14:07:26 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    jobid: 59
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A03v1_grac_868_S26_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=4096, disk_mib=3907, tmpdir=<TBD>

Submitted job 59 with external jobid '65586885'.
[Mon Aug  7 14:07:36 2023]
Error in rule compute_d4:
    jobid: 56
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586860

Error executing rule compute_d4 on cluster (jobid: 56, external: 65586860, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.56.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 56.
Select jobs to execute...

[Mon Aug  7 14:07:36 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    jobid: 56
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_815_S10_L004
    threads: 4
    resources: mem_mb=8000, mem_mib=7630, disk_mb=7473, disk_mib=7127, tmpdir=<TBD>

Submitted job 56 with external jobid '65586887'.
[Mon Aug  7 14:07:49 2023]
Error in rule create_gvcf_intervals:
    jobid: 79
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/abb557a3ad4a64770d7de92755c7727c_
    shell:
        
        gatk SplitIntervals -L results/GCA_026413385.1/intervals/master_interval_list.list         -O results/GCA_026413385.1/intervals/gvcf_intervals -R results/GCA_026413385.1/data/genome/GCA_026413385.1.fna -scatter 200         -mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION         --interval-merging-rule OVERLAPPING_ONLY  &> logs/GCA_026413385.1/gvcf_intervals/log.txt
        ls -l results/GCA_026413385.1/intervals/gvcf_intervals/*scattered.interval_list > results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586858

Error executing rule create_gvcf_intervals on cluster (jobid: 79, external: 65586858, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.create_gvcf_intervals.79.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 79.
Select jobs to execute...

[Mon Aug  7 14:07:49 2023]
checkpoint create_gvcf_intervals:
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt
    jobid: 79
    benchmark: benchmarks/GCA_026413385.1/gvcf_intervals/benchmark.txt
    reason: Missing output files: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
    wildcards: refGenome=GCA_026413385.1
    resources: mem_mb=1197, mem_mib=1142, disk_mb=1197, disk_mib=1142, tmpdir=<TBD>
DAG of jobs will be updated after completion.

Submitted job 79 with external jobid '65586888'.
[Mon Aug  7 14:08:02 2023]
Error in rule compute_d4:
    jobid: 61
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586881

Error executing rule compute_d4 on cluster (jobid: 61, external: 65586881, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.61.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 61.
Select jobs to execute...

[Mon Aug  7 14:08:02 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    jobid: 61
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=5317, disk_mib=5071, tmpdir=<TBD>

[Mon Aug  7 14:08:02 2023]
Error in rule compute_d4:
    jobid: 57
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586882

Error executing rule compute_d4 on cluster (jobid: 57, external: 65586882, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.57.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 61 with external jobid '65586892'.
Trying to restart job 57.
Select jobs to execute...

[Mon Aug  7 14:08:04 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    jobid: 57
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_864_S1_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=3368, disk_mib=3212, tmpdir=<TBD>

Submitted job 57 with external jobid '65586894'.
[Mon Aug  7 14:08:16 2023]
Error in rule compute_d4:
    jobid: 58
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586873

Error executing rule compute_d4 on cluster (jobid: 58, external: 65586873, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.58.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 58.
Select jobs to execute...

[Mon Aug  7 14:08:16 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    jobid: 58
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=8218, disk_mib=7838, tmpdir=<TBD>

[Mon Aug  7 14:08:16 2023]
Error in rule compute_d4:
    jobid: 63
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586874

Error executing rule compute_d4 on cluster (jobid: 63, external: 65586874, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.63.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:08:16 2023]
Error in rule compute_d4:
    jobid: 62
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586875

Error executing rule compute_d4 on cluster (jobid: 62, external: 65586875, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.62.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:08:17 2023]
Error in rule compute_d4:
    jobid: 60
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586876

Error executing rule compute_d4 on cluster (jobid: 60, external: 65586876, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.60.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:08:17 2023]
Error in rule compute_d4:
    jobid: 64
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586883

Error executing rule compute_d4 on cluster (jobid: 64, external: 65586883, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.64.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 58 with external jobid '65586901'.
Trying to restart job 63.
Trying to restart job 62.
Trying to restart job 60.
Trying to restart job 64.
Select jobs to execute...

[Mon Aug  7 14:08:17 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    jobid: 63
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A07v1_coca_846_S58_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=1716, disk_mib=1637, tmpdir=<TBD>

[Mon Aug  7 14:08:17 2023]
Error in rule compute_d4:
    jobid: 59
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586885

Error executing rule compute_d4 on cluster (jobid: 59, external: 65586885, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.59.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 63 with external jobid '65586902'.

[Mon Aug  7 14:08:19 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    jobid: 64
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A08v1_novo_777_S66_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=5604, disk_mib=5345, tmpdir=<TBD>

Submitted job 64 with external jobid '65586903'.

[Mon Aug  7 14:08:20 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    jobid: 62
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A06v1_grac_794_S50_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=6400, disk_mib=6104, tmpdir=<TBD>

Submitted job 62 with external jobid '65586904'.

[Mon Aug  7 14:08:21 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    jobid: 60
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=9187, disk_mib=8762, tmpdir=<TBD>

Submitted job 60 with external jobid '65586905'.
Trying to restart job 59.
Select jobs to execute...

[Mon Aug  7 14:08:22 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    jobid: 59
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A03v1_grac_868_S26_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=4096, disk_mib=3907, tmpdir=<TBD>

Submitted job 59 with external jobid '65586906'.
[Mon Aug  7 14:08:28 2023]
Error in rule compute_d4:
    jobid: 61
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586892

Error executing rule compute_d4 on cluster (jobid: 61, external: 65586892, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.61.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 61.
Select jobs to execute...

[Mon Aug  7 14:08:28 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    jobid: 61
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=5317, disk_mib=5071, tmpdir=<TBD>

[Mon Aug  7 14:08:29 2023]
Error in rule compute_d4:
    jobid: 56
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586887

Error executing rule compute_d4 on cluster (jobid: 56, external: 65586887, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.56.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 61 with external jobid '65586910'.
Trying to restart job 56.
Select jobs to execute...

[Mon Aug  7 14:08:30 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    jobid: 56
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_815_S10_L004
    threads: 4
    resources: mem_mb=12000, mem_mib=11445, disk_mb=7473, disk_mib=7127, tmpdir=<TBD>

Submitted job 56 with external jobid '65586911'.
[Mon Aug  7 14:08:42 2023]
Error in rule create_gvcf_intervals:
    jobid: 79
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/abb557a3ad4a64770d7de92755c7727c_
    shell:
        
        gatk SplitIntervals -L results/GCA_026413385.1/intervals/master_interval_list.list         -O results/GCA_026413385.1/intervals/gvcf_intervals -R results/GCA_026413385.1/data/genome/GCA_026413385.1.fna -scatter 200         -mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION         --interval-merging-rule OVERLAPPING_ONLY  &> logs/GCA_026413385.1/gvcf_intervals/log.txt
        ls -l results/GCA_026413385.1/intervals/gvcf_intervals/*scattered.interval_list > results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586888

Error executing rule create_gvcf_intervals on cluster (jobid: 79, external: 65586888, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.create_gvcf_intervals.79.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 79.
Select jobs to execute...

[Mon Aug  7 14:08:42 2023]
checkpoint create_gvcf_intervals:
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt
    jobid: 79
    benchmark: benchmarks/GCA_026413385.1/gvcf_intervals/benchmark.txt
    reason: Missing output files: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
    wildcards: refGenome=GCA_026413385.1
    resources: mem_mb=1197, mem_mib=1142, disk_mb=1197, disk_mib=1142, tmpdir=<TBD>
DAG of jobs will be updated after completion.

Submitted job 79 with external jobid '65586916'.
[Mon Aug  7 14:09:08 2023]
Error in rule compute_d4:
    jobid: 61
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A05v1_ipad_772_S42_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586910

Error executing rule compute_d4 on cluster (jobid: 61, external: 65586910, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.61.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:09:09 2023]
Error in rule compute_d4:
    jobid: 56
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586911

Error executing rule compute_d4 on cluster (jobid: 56, external: 65586911, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.56.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 56.
Select jobs to execute...

[Mon Aug  7 14:09:09 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    jobid: 56
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_815_S10_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=7473, disk_mib=7127, tmpdir=<TBD>

[Mon Aug  7 14:09:10 2023]
Error in rule compute_d4:
    jobid: 64
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586903

Error executing rule compute_d4 on cluster (jobid: 64, external: 65586903, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.64.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:09:10 2023]
Error in rule compute_d4:
    jobid: 62
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586904

Error executing rule compute_d4 on cluster (jobid: 62, external: 65586904, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.62.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:09:11 2023]
Error in rule compute_d4:
    jobid: 60
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586905

Error executing rule compute_d4 on cluster (jobid: 60, external: 65586905, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.60.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 56 with external jobid '65586922'.
Trying to restart job 64.
Trying to restart job 62.
Trying to restart job 60.
Select jobs to execute...

[Mon Aug  7 14:09:11 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    jobid: 64
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A08v1_novo_777_S66_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=5604, disk_mib=5345, tmpdir=<TBD>

[Mon Aug  7 14:09:11 2023]
Error in rule compute_d4:
    jobid: 59
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586906

Error executing rule compute_d4 on cluster (jobid: 59, external: 65586906, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.59.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 64 with external jobid '65586923'.

[Mon Aug  7 14:09:12 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    jobid: 62
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A06v1_grac_794_S50_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=6400, disk_mib=6104, tmpdir=<TBD>

Submitted job 62 with external jobid '65586924'.

[Mon Aug  7 14:09:15 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    jobid: 60
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=9187, disk_mib=8762, tmpdir=<TBD>

Submitted job 60 with external jobid '65586927'.
Trying to restart job 59.
Select jobs to execute...

[Mon Aug  7 14:09:16 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    jobid: 59
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A03v1_grac_868_S26_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=4096, disk_mib=3907, tmpdir=<TBD>

Submitted job 59 with external jobid '65586930'.
[Mon Aug  7 14:09:22 2023]
Error in rule compute_d4:
    jobid: 58
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586901

Error executing rule compute_d4 on cluster (jobid: 58, external: 65586901, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.58.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 58.
Select jobs to execute...

[Mon Aug  7 14:09:22 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    jobid: 58
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=8218, disk_mib=7838, tmpdir=<TBD>

[Mon Aug  7 14:09:22 2023]
Error in rule compute_d4:
    jobid: 57
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586894

Error executing rule compute_d4 on cluster (jobid: 57, external: 65586894, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.57.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:09:23 2023]
Error in rule compute_d4:
    jobid: 63
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586902

Error executing rule compute_d4 on cluster (jobid: 63, external: 65586902, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.63.sh). For error details see the cluster log and the log files of the involved rule(s).
Submitted job 58 with external jobid '65586931'.
Trying to restart job 57.
Trying to restart job 63.
Select jobs to execute...

[Mon Aug  7 14:09:24 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    jobid: 57
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A01v1_coca_864_S1_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=3368, disk_mib=3212, tmpdir=<TBD>

Submitted job 57 with external jobid '65586932'.

[Mon Aug  7 14:09:25 2023]
rule compute_d4:
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    jobid: 63
    benchmark: benchmarks/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
    reason: Missing output files: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    wildcards: refGenome=GCA_026413385.1, sample=PREP0329_DWhit15901A_A07v1_coca_846_S58_L004
    threads: 4
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1716, disk_mib=1637, tmpdir=<TBD>

Submitted job 63 with external jobid '65586933'.
[Mon Aug  7 14:09:47 2023]
Error in rule compute_d4:
    jobid: 56
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_815_S10_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586922

Error executing rule compute_d4 on cluster (jobid: 56, external: 65586922, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.56.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:09:48 2023]
Error in rule compute_d4:
    jobid: 64
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A08v1_novo_777_S66_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586923

Error executing rule compute_d4 on cluster (jobid: 64, external: 65586923, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.64.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:00 2023]
Error in rule create_gvcf_intervals:
    jobid: 79
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/abb557a3ad4a64770d7de92755c7727c_
    shell:
        
        gatk SplitIntervals -L results/GCA_026413385.1/intervals/master_interval_list.list         -O results/GCA_026413385.1/intervals/gvcf_intervals -R results/GCA_026413385.1/data/genome/GCA_026413385.1.fna -scatter 200         -mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION         --interval-merging-rule OVERLAPPING_ONLY  &> logs/GCA_026413385.1/gvcf_intervals/log.txt
        ls -l results/GCA_026413385.1/intervals/gvcf_intervals/*scattered.interval_list > results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586916

Error executing rule create_gvcf_intervals on cluster (jobid: 79, external: 65586916, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.create_gvcf_intervals.79.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 79.
Select jobs to execute...

[Mon Aug  7 14:10:00 2023]
checkpoint create_gvcf_intervals:
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt
    jobid: 79
    benchmark: benchmarks/GCA_026413385.1/gvcf_intervals/benchmark.txt
    reason: Missing output files: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
    wildcards: refGenome=GCA_026413385.1
    resources: mem_mb=1197, mem_mib=1142, disk_mb=1197, disk_mib=1142, tmpdir=<TBD>
DAG of jobs will be updated after completion.

Submitted job 79 with external jobid '65586968'.
[Mon Aug  7 14:10:13 2023]
Error in rule compute_d4:
    jobid: 58
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A02v1_grac_1465_S18_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586931

Error executing rule compute_d4 on cluster (jobid: 58, external: 65586931, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.58.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:13 2023]
Error in rule compute_d4:
    jobid: 62
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A06v1_grac_794_S50_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586924

Error executing rule compute_d4 on cluster (jobid: 62, external: 65586924, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.62.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:13 2023]
Error in rule compute_d4:
    jobid: 60
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A04v1_coca_1493_S34_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586927

Error executing rule compute_d4 on cluster (jobid: 60, external: 65586927, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.60.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:14 2023]
Error in rule compute_d4:
    jobid: 59
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A03v1_grac_868_S26_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586930

Error executing rule compute_d4 on cluster (jobid: 59, external: 65586930, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.59.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:14 2023]
Error in rule compute_d4:
    jobid: 57
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A01v1_coca_864_S1_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586932

Error executing rule compute_d4 on cluster (jobid: 57, external: 65586932, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.57.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:10:14 2023]
Error in rule compute_d4:
    jobid: 63
    input: results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam, results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam.bai
    output: results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.global.dist.txt, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.per-base.d4, results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.mosdepth.summary.txt
    log: logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/9103abe48335cebba4f9cf1c4e6c647e_
    shell:
        mosdepth --d4 -t 4 results/GCA_026413385.1/callable_sites/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004 results/GCA_026413385.1/bams/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004_final.bam &> logs/GCA_026413385.1/compute_d4/PREP0329_DWhit15901A_A07v1_coca_846_S58_L004.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586933

Error executing rule compute_d4 on cluster (jobid: 63, external: 65586933, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.compute_d4.63.sh). For error details see the cluster log and the log files of the involved rule(s).
[Mon Aug  7 14:11:16 2023]
Error in rule create_gvcf_intervals:
    jobid: 79
    input: results/GCA_026413385.1/data/genome/GCA_026413385.1.fna, results/GCA_026413385.1/data/genome/GCA_026413385.1.fna.fai, results/GCA_026413385.1/data/genome/GCA_026413385.1.dict, results/GCA_026413385.1/intervals/master_interval_list.list
    output: results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt, results/GCA_026413385.1/intervals/gvcf_intervals
    log: logs/GCA_026413385.1/gvcf_intervals/log.txt (check log file(s) for error details)
    conda-env: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/conda/abb557a3ad4a64770d7de92755c7727c_
    shell:
        
        gatk SplitIntervals -L results/GCA_026413385.1/intervals/master_interval_list.list         -O results/GCA_026413385.1/intervals/gvcf_intervals -R results/GCA_026413385.1/data/genome/GCA_026413385.1.fna -scatter 200         -mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION         --interval-merging-rule OVERLAPPING_ONLY  &> logs/GCA_026413385.1/gvcf_intervals/log.txt
        ls -l results/GCA_026413385.1/intervals/gvcf_intervals/*scattered.interval_list > results/GCA_026413385.1/intervals/gvcf_intervals/intervals.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 65586968

Error executing rule create_gvcf_intervals on cluster (jobid: 79, external: 65586968, jobscript: /n/holyscratch01/davis_lab/dwhite/snpArcher/.snakemake/tmp.71lacvnq/snakejob.create_gvcf_intervals.79.sh). For error details see the cluster log and the log files of the involved rule(s).
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-08-07T140601.982628.snakemake.log