DAY-EC activated.
DAY-EC activated.
            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/summary.txt \
              TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA \
              /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" \
              ug \
              na \
              sentdug \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv
            

[Sat May 30 08:23:55 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.altair-v1.1.parse_vcfeval_summary.log
    jobid: 11
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.altair-v1.1.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/summary.txt
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, 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="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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"

            mkdir -p "$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/summary.txt \
              TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA \
              /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" \
              ug \
              na \
              sentdug \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv
            

[Sat May 30 08:23:55 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/summary.txt, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/clinvar_genes/HG003.bed
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.clinvar_genes.parse_vcfeval_summary.log
    jobid: 13
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.clinvar_genes.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/summary.txt
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=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="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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"

            mkdir -p "$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/summary.txt \
              TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA \
              /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" \
              ug \
              na \
              sentdug \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv
            

[Sat May 30 08:23:55 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.parse_vcfeval_summary.log
    jobid: 21
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, 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="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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"

            mkdir -p "$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt \
              TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA \
              /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" \
              ug \
              na \
              sentdug \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
            

[Sat May 30 08:23:55 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.fofn, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.concordance.log
    jobid: 10
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug
    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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.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=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.concordance.log;
            

[Sat May 30 08:23:55 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 9
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_altair-v1.1/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/snv_TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/concordance.done
    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                          1             96             96
alignstats_compile                  1              2              2
alignstats_gather                   1              1              1
finish_align_stats                  1              2              2
no_dedup_cram                       1              1              1
parse_vcfeval_summary_roi           6             16             16
pre_prep_ultima_cram                1             48             48
prep_for_concordance_check          1              8              8
prep_sentdug_chunkdirs              1              1              1
produce_alignstats                  1              1              1
produce_na_dedup_cram               1              1              1
produce_sentdug_snv_vcf             1              1              1
produce_snv_concordances            1              1              1
rtg_vcfeval_roi                     6             16             16
sent_snv_ug                         1            192            192
sentdug_concat_fofn                 1              1              1
sentdug_concat_index_chunks         1             64             64
sentdug_sort_index_chunk_vcf        1             64             64
total                              28              1            192

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        alignstats, alignstats_compile, alignstats_gather, finish_align_stats, no_dedup_cram, parse_vcfeval_summary_roi, prep_for_concordance_check, prep_sentdug_chunkdirs, produce_alignstats, produce_na_dedup_cram, produce_sentdug_snv_vcf, produce_snv_concordances, rtg_vcfeval_roi, sent_snv_ug, sentdug_concat_fofn, sentdug_concat_index_chunks, sentdug_sort_index_chunk_vcf
    missing output files:
        alignstats, alignstats_compile, alignstats_gather, finish_align_stats, no_dedup_cram, parse_vcfeval_summary_roi, pre_prep_ultima_cram, prep_for_concordance_check, prep_sentdug_chunkdirs, produce_na_dedup_cram, produce_sentdug_snv_vcf, produce_snv_concordances, rtg_vcfeval_roi, sen--output truncated--
