DAY-EC activated.
DAY-EC activated.
    jobid: 15
    benchmark: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/benchmarks/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.clinvar_genes.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/summary.txt
    wildcards: sample=TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO, alnr=sentmm2, ddup=na, snv=sentdpb, 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="$(dirname results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/summary.txt \
              TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO \
              /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" \
              sentmm2 \
              na \
              sentdpb \
              > results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv
            

[Sat May 30 10:25:51 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.altair-v1.1.parse_vcfeval_summary.log
    jobid: 13
    benchmark: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/benchmarks/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.altair-v1.1.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/summary.txt
    wildcards: sample=TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO, alnr=sentmm2, ddup=na, snv=sentdpb, 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="$(dirname results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/summary.txt \
              TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO \
              /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" \
              sentmm2 \
              na \
              sentdpb \
              > results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv
            

[Sat May 30 10:25:51 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.giabHC.parse_vcfeval_summary.log
    jobid: 17
    benchmark: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/benchmarks/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.giabHC.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/summary.txt
    wildcards: sample=TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO, alnr=sentmm2, ddup=na, snv=sentdpb, 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="$(dirname results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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"

            mkdir -p "$(dirname results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv)"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/summary.txt \
              TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO \
              /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" \
              sentmm2 \
              na \
              sentdpb \
              > results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv
            

[Sat May 30 10:25:51 2026]
localrule alignstats_compile:
    input: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    output: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv, results/day/hg38_broad/other_reports/alignstats_csummary.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_compile.log
    jobid: 3
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_smmary_compile.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv; Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    threads: 2
    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
        python workflow/scripts/compile_alignstats.py           --mdir results/day/hg38_broad/           --log results/day/hg38_broad/logs/alignstats_summary_compile.log           --bsummary results/day/hg38_broad/other_reports/alignstats_bsummary.tsv           --csummary results/day/hg38_broad/other_reports/alignstats_csummary.tsv           --combo results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv           --generalstats results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv
        

[Sat May 30 10:25:51 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.snv.sort.vcf.gz, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC_x_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38_m_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.done, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.fofn, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.concordance.log
    jobid: 12
    benchmark: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/benchmarks/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC_x_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.snv.sort.vcf.gz, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38_m_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv
    wildcards: sample=TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO, alnr=sentmm2, ddup=na, snv=sentdpb
    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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.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=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC_x_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38_m_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/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/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/logs/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO.sentmm2.na.sentdpb.concordance.log;
            
Would remove temporary output results/day/hg38_broad/other_reports/alignstats_csummary.tsv

[Sat May 30 10:25:51 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.done, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC_x_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38_m_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 11
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC_x_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/concordance.done, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_hg38_m_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_altair-v1.1/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_clinvar_genes/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO/align/sentmm2/na/snv/sentdpb/concordance/_giabHC/snv_TVBPB5X-HG003-5x-1-D0-PF-PACBIO-REVIO_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=

[Sat May 30 10:25:51 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=

Would remove temporary output results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
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
prep_for_concordance_check        1              8              8
produce_alignstats                1              1              1
produce_na_dedup_cram             1              1              1
produce_sentdpb_snv_vcf           1              1              1
produce_sentmm2_align             1              1              1
produce_snv_concordances          1              1              1
rtg_vcfeval_roi                   6             16             16
sent_snv_pacbio      --output truncated--
