DAY-EC activated.
DAY-EC activated.
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.log 2>&1
        bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.vcf.gz | wc -l | awk '{print $1}' > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.vcf.gz.record_count
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.vcf.gz
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.input.vcf.gz.tbi
        
Submitted job 29 with external jobid '60'.

[Fri May 29 21:17:31 2026]
rule vep_chromosome_input:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.record_count
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.log
    jobid: 72
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.vep_input.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr22
    resources: mem_mb=4000, mem_mib=3815, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz) $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.log)
        if bcftools index -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | cut -f1 | grep -Fxq "chr22"; then
            bcftools view -r chr22 -O z -o results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.log 2>&1
        else
            bcftools view -h results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | bgzip -c > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz
        fi
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.log 2>&1
        bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz | wc -l | awk '{print $1}' > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.record_count
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.input.vcf.gz.tbi
        
Submitted job 72 with external jobid '61'.

[Fri May 29 21:17:31 2026]
rule vep_chromosome_input:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.record_count
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.log
    jobid: 66
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep_input.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr19
    resources: mem_mb=4000, mem_mib=3815, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz) $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.log)
        if bcftools index -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | cut -f1 | grep -Fxq "chr19"; then
            bcftools view -r chr19 -O z -o results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.log 2>&1
        else
            bcftools view -h results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | bgzip -c > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz
        fi
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.log 2>&1
        bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz | wc -l | awk '{print $1}' > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.record_count
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.tbi
        
Submitted job 66 with external jobid '62'.

[Fri May 29 21:17:31 2026]
rule vep_chromosome_input:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.record_count
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.log
    jobid: 50
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep_input.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr11
    resources: mem_mb=4000, mem_mib=3815, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz) $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.log)
        if bcftools index -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | cut -f1 | grep -Fxq "chr11"; then
            bcftools view -r chr11 -O z -o results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.log 2>&1
        else
            bcftools view -h results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | bgzip -c > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz
        fi
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.log 2>&1
        bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz | wc -l | awk '{print $1}' > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.record_count
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.tbi
        
Submitted job 50 with external jobid '63'.

[Fri May 29 21:17:31 2026]
rule vep_chromosome_input:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz.record_count
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.log
    jobid: 38
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.vep_input.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.input_contigs.ok
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr5
    resources: mem_mb=4000, mem_mib=3815, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz) $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.log)
        if bcftools index -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | cut -f1 | grep -Fxq "chr5"; then
            bcftools view -r chr5 -O z -o results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.log 2>&1
        else
            bcftools view -h results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | bgzip -c > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz
        fi
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.log 2>&1
        bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.input.vcf.gz | wc -l | awk '{print $1}' > results/day/hg38_broad/TVBILMN5X-H--output truncated--
