DAY-EC activated.
DAY-EC activated.
rule vep_concat_index_chunks:
    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.concat.vcf.gz.fofn, 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, 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
    output: 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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi, 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.done
    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: 7
    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/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/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/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/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/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/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/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/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/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.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, 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/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/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/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/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/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/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/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/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/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.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-NOVA--output truncated--
