DAY-EC activated.
DAY-EC activated.
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log
    jobid: 58
    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.vep_concat.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.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/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrX/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrX.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrM/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrM.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.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.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.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrX/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrX.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.vep.vcf.gz.record_count, 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.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr20.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.vcf.gz.fofn, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr20.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrY/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrY.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.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.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.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrM/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrM.vep.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.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrY/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrY.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.vep.vcf.gz.record_count, 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, 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.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.input.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.vep.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.record_count
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd
    threads: 16
    resources: mem_mb=32000, mem_mib=30518, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i128, vcpu=16, 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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz) $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log)
        input_count=$(awk '{s+=$1} END {print s+0}' 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 results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.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.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.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.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.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.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr20.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.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.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrX/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrX.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrY/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrY.input.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrM/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrM.input.vcf.gz.record_count)
        ann_count=$(awk '{s+=$1} END {print s+0}' 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.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.vep.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.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.vep.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.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.vep.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.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr20.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.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.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrX/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrX.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrY/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrY.vep.vcf.gz.record_count results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrM/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrM.vep.vcf.gz.record_count)
        if [ "$input_count" -ne "$ann_count" ]; then
            echo "ERROR: VEP annotated variant count ($ann_count) does not match input chunk count ($input_count)" >&2
            exit 2
        fi
        bcftools concat -a -d all --threads 16 -f results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.vcf.gz.fofn -O z -o results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.temp.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log 2>&1
        mv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.temp.vcf.gz results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz
        tabix -f -p vcf results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log 2>&1
        final_count=$(bcftools view -H results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz | wc -l | awk '{print $1}')
        if [ "$final_count" -ne "$input_count" ]; then
            echo "ERROR: final VEP VCF count ($final_count) does not match input count ($input_count)" >&2
            exit 2
        fi
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz
        test -s results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi


[Fri May 29 20:28:48 2026]
localrule vep_annotation_gather:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi
    output: results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv
    jobid: 57
    reason: Missing output files: results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

[Fri May 29 20:28:48 2026]
localrule produce_vep:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi, results/day/hg38_broad/other_reports--output truncated--
