DAY-EC activated.
DAY-EC activated.
        mv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.vcf.gz.fofn.tmp results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.vcf.gz.fofn


[Fri May 29 23:31:02 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 7
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv
    priority: 48
    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 23:31:02 2026]
rule vep_concat_index_chunks:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.vcf.gz.fofn, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr1/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr1.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr2/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr2.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr3/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr3.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr4/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr4.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr5/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr5.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr6/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr6.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr7/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr7.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr8/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr8.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr9/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr9.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr10/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr10.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr11/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr11.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr12/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr12.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr13/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr13.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr14/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr14.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr15/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr15.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr16/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr16.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr17/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr17.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr18/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr18.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr19/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr19.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr20/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr20.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr21/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr21.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr22/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr22.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrX/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrX.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrY/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrY.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrM/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrM.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr1/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr1.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr2/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr3/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr3.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr4/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr5/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr5.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr6/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr7/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr8/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr8.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr9/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr10/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr11/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr11.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr12/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr13/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr14/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr14.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr15/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr16/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr17/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr18/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr19/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr20/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr20.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr21/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr21.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr22/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr22.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrX/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrX.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrY/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrY.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrM/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrM.vep.vcf.gz.record_count
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.done
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/log/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.log
    jobid: 51
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep_concat.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr22/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr22.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr15/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr15.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr13/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr11/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr11.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr7/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr12/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr7/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr7.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr21/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr21.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr4/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr4.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr6/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr6.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr1/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr1.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr16/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr16.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr18/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr18.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr12/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr12.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr15/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr2/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr2.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrM/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrM.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr21/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr21.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr3/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr3.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrY/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrY.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr10/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr19/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrX/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrX.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr20/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr20.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.vcf.gz.fofn, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr17/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr17.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr9/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr5/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr5.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr2/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr8/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr8.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr20/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr20.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr13/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr13.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr5/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr5.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr6/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr14/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr14.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr1/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr1.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrM/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrM.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr11/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr11.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr18/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr8/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr8.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr19/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr19.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr9/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr9.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr14/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr14.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr4/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr10/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr10.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrY/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrY.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr17/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr22/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr22.input.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr16/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr3/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr3.vep.vcf.gz.record_count, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chrX/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chrX.input.vcf.gz.record_count
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug
    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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.vcf.gz) $(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/log/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.vep.concat.log)
        input_count=$(awk '{s+=$1} END {print s+0}' results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr1/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr1.input.vcf.gz.record_count results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr2/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr2.input.vcf.gz.record_count results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr3/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.chr3.input.vcf.gz.record_count results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/vep/chunks/chr4/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.n--output truncated--
