DAY-EC activated.
DAY-EC activated.
              ont \
              dmd \
              sentdhiomr \
              > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.giabHC.parse_vcfeval_summary.log 2>&1

            # Hard check: the legacy script should have written the MQC output where we declared it.
            test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv
            

[Fri May 29 23:38:15 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38/HG003.bed
    output: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38.parse_vcfeval_summary.log
    jobid: 741
    benchmark: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/summary.txt
    wildcards: sample=TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, snv=sentdhiomr, cmpfootprint=hg38
    threads: 16
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


            set -euo pipefail

            outdir="$(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$outdir/vcfeval_summary.parsed.tsv"

            # Keep mean depth behavior identical to the current rule (effectively NA/-1).
            allvar_mean_dp="na"

            # Prevent parse script from over-threading bcftools when many ROIs run concurrently.
            export DAYLILY_BCFTOOLS_THREADS="16"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/summary.txt \
              TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38/HG003.bed \
              hg38 \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              ont \
              dmd \
              sentdhiomr \
              > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38.parse_vcfeval_summary.log 2>&1

            # Hard check: the legacy script should have written the MQC output where we declared it.
            test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv
            

[Fri May 29 23:38:15 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.bed
    output: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38_m_giabHC.parse_vcfeval_summary.log
    jobid: 743
    benchmark: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38_m_giabHC.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/summary.txt
    wildcards: sample=TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, snv=sentdhiomr, cmpfootprint=hg38_m_giabHC
    threads: 16
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


            set -euo pipefail

            outdir="$(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$outdir/vcfeval_summary.parsed.tsv"

            # Keep mean depth behavior identical to the current rule (effectively NA/-1).
            allvar_mean_dp="na"

            # Prevent parse script from over-threading bcftools when many ROIs run concurrently.
            export DAYLILY_BCFTOOLS_THREADS="16"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/summary.txt \
              TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.bed \
              hg38_m_giabHC \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              ont \
              dmd \
              sentdhiomr \
              > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.hg38_m_giabHC.parse_vcfeval_summary.log 2>&1

            # Hard check: the legacy script should have written the MQC output where we declared it.
            test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
            

[Fri May 29 23:38:15 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/altair-v1.1/HG003.bed
    output: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.altair-v1.1.parse_vcfeval_summary.log
    jobid: 733
    benchmark: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.altair-v1.1.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/summary.txt
    wildcards: sample=TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, snv=sentdhiomr, cmpfootprint=altair-v1.1
    threads: 16
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


            set -euo pipefail

            outdir="$(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$outdir/vcfeval_summary.parsed.tsv"

            # Keep mean depth behavior identical to the current rule (effectively NA/-1).
            allvar_mean_dp="na"

            # Prevent parse script from over-threading bcftools when many ROIs run concurrently.
            export DAYLILY_BCFTOOLS_THREADS="16"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/summary.txt \
              TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/altair-v1.1/HG003.bed \
              altair-v1.1 \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              ont \
              dmd \
              sentdhiomr \
              > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.altair-v1.1.parse_vcfeval_summary.log 2>&1

            # Hard check: the legacy script should have written the MQC output where we declared it.
            test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv
            

[Fri May 29 23:38:15 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.fofn, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concordance.log
    jobid: 4
    benchmark: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi
    wildcards: sample=TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, snv=sentdhiomr
    priority: 48
    threads: 8
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


            set +euo pipefail;

            mkdir -p $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concordance.log);

            utc_ts=$(date -u +%Y-%m-%dT%H:%M:%SZ);

            # Write informational fofn
            {
                echo "# Refactor: per-ROI jobs are scheduled by Snakemake; this file is informational.";
                echo "# generated_at_utc=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.fofn;

            # Write informational fin.cmds
            {
                echo "# Refactor: see Snakemake DAG for exact commands.";
                echo "# generated_at_utc=$utc_ts";
            } > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.fin.cmds;

            # SKIPPED sentinel if no mqcs
            if [ "6" -eq 0 ]; then
                echo "No truthset ROI directories found; concordance skipped." > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done.SKIPPED;
            fi;

            # Log
            echo "Concordance sentinel complete. footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC mqcs=6" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/logs/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.concordance.log;
            

[Fri May 29 23:38:15 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 3
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_altair-v1.1/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/concordance.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_hg38_m_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_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=

Job stats:
job                               count    min threads    max threads
------------------------------  -------  -------------  -------------
parse_vcfeval_summary_roi             6             16             16
pre_prep_ont_cram                     1             48             48
pre_prep_raw_fq                       1              1              1
prep_for_concordance_check            1              8              8
prep_results_dirs                     1              1              1
produce_sentdhiomr_snv_vcf            1              1              1
produce_sentdhiomr_sv                 1              1              1
produce_snv_concordances  --output truncated--
