DAY-EC activated.
DAY-EC activated.
Provided resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, threads=1, time=5440, vcpu=1
Select jobs to execute...
[Fri May 29 22:18:16 2026]
Finished job 82.
88 of 106 steps (83%) done
[Fri May 29 22:18:34 2026]
Finished job 46.
89 of 106 steps (84%) done
[Fri May 29 22:18:44 2026]
Finished job 42.
90 of 106 steps (85%) done
[Fri May 29 22:18:54 2026]
Finished job 48.
91 of 106 steps (86%) done
Select jobs to execute...

[Fri May 29 22:18:54 2026]
localrule vep_concat_fofn:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr1/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr1.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr4/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr4.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr6/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr6.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr8/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr8.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr10/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr10.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr12/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr12.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr14/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr14.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr16/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr16.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr17/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr17.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr18/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr18.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr19/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr19.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr20/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr20.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr21/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr21.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr22/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr22.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrX/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrX.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrY/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrY.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrM/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrM.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr1/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr1.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr4/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr6/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr8/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr8.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr10/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr12/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr14/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr14.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr16/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr17/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr18/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr19/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr20/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr20.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr21/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr21.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr22/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr22.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrX/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrX.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrY/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrY.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrM/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrM.vep.vcf.gz.record_count
    output: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat.vcf.gz.fofn
    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat_fofn.log
    jobid: 2
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat.vcf.gz.fofn; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr10/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr10.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr8/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr8.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr14/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr14.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr19/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr19.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr21/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr21.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrM/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrM.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr20/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr20.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr22/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr22.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrX/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrX.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr1/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr1.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr4/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr4.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr21/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr21.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrY/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrY.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr18/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr18.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr14/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr14.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr10/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr8/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr8.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr6/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr6.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrY/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrY.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr17/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr4/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr6/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr18/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr22/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr22.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr12/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr20/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr20.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr16/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr16.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr12/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr12.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr16/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrX/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrX.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr19/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr17/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr17.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr1/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr1.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chrM/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrM.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.vep.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.vep.vcf.gz.tbi
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na, snv=sentdont
    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=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat.vcf.gz.fofn) $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat_fofn.log)
        : > results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep.concat.vcf.gz.fofn.tmp
        for count_path in results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr1/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr1.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr4/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr4.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr6/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr6.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr8/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr8.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr10/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr10.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr12/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr12.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr14/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr14.vep.vcf.gz.record_count results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/vep/chunks/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.vep.vcf.gz.record_count results/day/hg38_broad/TVBON--output truncated--
