DAY-EC activated.
DAY-EC activated.
    output: results/day/hg38_broad/other_reports/alignment_qc_outputs_mqc.tsv
    log: results/day/hg38_broad/other_reports/logs/alignment_qc_outputs_custom_data.log
    jobid: 23
    reason: Missing output files: results/day/hg38_broad/other_reports/alignment_qc_outputs_mqc.tsv; Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/samtools_metrics_gather.done, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/norm_cov_eveness/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.md, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/samtmetrics/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.complete, results/day/hg38_broad/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.summary.txt, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft.done, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/contam/gatk/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.gatk.tsv
    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/other_reports/alignment_qc_outputs_mqc.tsv) $(dirname results/day/hg38_broad/other_reports/logs/alignment_qc_outputs_custom_data.log)
        python workflow/scripts/multiqc_custom_output_inventory.py           --stage alignment_qc           --output results/day/hg38_broad/other_reports/alignment_qc_outputs_mqc.tsv           results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv results/day/hg38_broad/other_reports/norm_cov_evenness_combo_mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/samtmetrics/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.complete results/day/hg38_broad/other_reports/samtools_metrics_gather.done results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.summary.txt results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft.done results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/norm_cov_eveness/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.md results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/contam/gatk/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.gatk.tsv > results/day/hg38_broad/other_reports/logs/alignment_qc_outputs_custom_data.log 2>&1


[Sat May 30 09:27:53 2026]
localrule produce_alignstats:
    input: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    jobid: 2
    reason: Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    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=

[Sat May 30 09:27:53 2026]
rule vep_concat_index_chunks:
    input: 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, 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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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.input.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/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.vcf.gz, 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.vcf.gz.tbi, 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.done
    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.log
    jobid: 34
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.vep_concat.bench.tsv
    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.vcf.gz.tbi; 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/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/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/chr19/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr19.input.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/chr7/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr7.input.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.input.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.input.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/chr5/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr5.input.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/chr18/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr18.input.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/chr15/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr15.input.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/chrY/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrY.input.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/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/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/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/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/chr3/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr3.input.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/chr9/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr9.input.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/chr13/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr13.input.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/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/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/chr22/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr22.input.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/chrX/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrX.input.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/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/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/chr11/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr11.input.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.input.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.input.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.input.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/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/chr2/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chr2.input.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.input.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/chrM/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.chrM.input.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.input.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.input.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.input.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.s--output truncated--
