DAY-EC activated.
DAY-EC activated.
            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/summary.txt \
              TVBCG5X-HG003-5x-1-D0-PF-CG-MGI \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/clinvar_genes/HG003.bed \
              clinvar_genes \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              sentcg \
              dmd \
              cgt7p \
              > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.clinvar_genes.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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv


[Sat May 30 07:29:11 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.bed
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.giabHC_x_clinvar_genes.parse_vcfeval_summary.log
    jobid: 28
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.giabHC_x_clinvar_genes.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, cmpfootprint=giabHC_x_clinvar_genes
    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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/summary.txt \
              TVBCG5X-HG003-5x-1-D0-PF-CG-MGI \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.bed \
              giabHC_x_clinvar_genes \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              sentcg \
              dmd \
              cgt7p \
              > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.giabHC_x_clinvar_genes.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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv


[Sat May 30 07:29:11 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.hg38.parse_vcfeval_summary.log
    jobid: 30
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.hg38.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, 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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/summary.txt \
              TVBCG5X-HG003-5x-1-D0-PF-CG-MGI \
              /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" \
              sentcg \
              dmd \
              cgt7p \
              > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv


[Sat May 30 07:29:11 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.giabHC.parse_vcfeval_summary.log
    jobid: 26
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.giabHC.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, cmpfootprint=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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/summary.txt \
              TVBCG5X-HG003-5x-1-D0-PF-CG-MGI \
              /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed \
              giabHC \
              HG003 \
              "$legacy_parsed" \
              "$allvar_mean_dp" \
              sentcg \
              dmd \
              cgt7p \
              > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv


[Sat May 30 07:29:11 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.done, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.fofn, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concordance.log
    jobid: 16
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_concordance.mqc.tsv
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p
    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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.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=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/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/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/logs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concordance.log;


[Sat May 30 07:29:11 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.done, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 15
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC_x_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/concordance.done, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_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
--------------------------  -------  -------------  -------------
alignstats                        2             96             96
alignstats_compile                1              2              2
alignstats_gather                 1              1              1
cgt7p_DNAscope                    1            192            192
cgt7p_concat_fofn                 1              1              1
cgt7p_concat_index_chunks         1             16             16
cgt7p_sort_index_chunk_vcf        1              1              1
doppelmark_dups                   1            192            192
finish_align_stats                2              2              2
no_dedup                          1              4              4
parse_vcfeval_summary_roi         6             16             16
pre_prep_raw_fq                   1              1              1
prep_cgt7p_chunkdirs              1              1              1
prep_for_concordance_check        1              8              8
prep_results_dirs                 1              1              1
produce_alignstats                1              1              1
produce_cgt7p_snv_vcf             1              1              1
produce_dmd_dedup_cram            1              1              1
produce_sentcg_align              1              1              1
produce_snv_concordances          1              1              1
rtg_vcfeval_roi                   6             16             16
sentieon_cgt7p_bwa_sort           1            192            192
stage_supporting_data             1              1              1
workflow_staging                  1              1              1
total                            36              1            192

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        alignstats, alignstats_compile, alignstats_gather, cgt7p_DNAscope, cgt7p_concat_fofn, cgt7p_concat_index_chunks, cgt7p_sort_index_chunk_vcf, doppelmark_dups, finish_align_stats, no_dedup, parse_vcfeval_summary_roi, prep_cgt7p_chunkdirs, prep_for_concordance_check, prep_results_dirs, produce_alignstats, produce_cgt7p_snv_vcf, produce_dmd_dedup_cram, produce_sentcg_align, produce_snv_concordances, rtg_vcfeval_roi, sentieon_cgt7p_bwa_sort, workflow_staging
    missing output files:
        alignstats, alignstats_compile, alignstats_gather, cgt7p_DNAscope, cgt7p_concat_fofn, cgt7p_concat_index_chunks, cgt7p_sort_index_chunk_vcf, doppelmark_dups, finish_align_stats, no_dedup, parse_vcfeval_summary_roi, pre_prep_raw_fq, prep_cgt7p_chunkdirs, prep_for_concordance_check, prep_results_dirs, produce_cgt7p_snv_vcf, produce_dmd_dedup_cram, produce_sentcg_align, produce_snv_concordances, rtg_vcfeval_roi, sentieon_cgt7p_bwa_sort, stage_supporting_data, workflow_staging

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
RETURN CODE: 0
[INFO] Workflow exited with status 0
DA--output truncated--
