DAY-EC activated.
DAY-EC activated.
            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/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)"

            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

Submitted job 31 with external jobid '4437'.
[Sat May 30 18:16:11 2026]
Finished job 26.
24 of 36 steps (67%) done
[Sat May 30 18:16:11 2026]
Finished job 34.
25 of 36 steps (69%) done
[Sat May 30 18:16:11 2026]
Finished job 24.
26 of 36 steps (72%) done
Select jobs to execute...

[Sat May 30 18:16:11 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/_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/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
    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.clinvar_genes.parse_vcfeval_summary.log
    jobid: 25
    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.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/_clinvar_genes/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_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/_clinvar_genes/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, 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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_clinvar_genes/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/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)"

            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

Submitted job 25 with external jobid '4438'.

[Sat May 30 18:16:11 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/_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/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
    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.altair-v1.1.parse_vcfeval_summary.log
    jobid: 23
    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.altair-v1.1.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/_altair-v1.1/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_altair-v1.1_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/_altair-v1.1/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, 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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_altair-v1.1/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/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)"

            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/_altair-v1.1/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/altair-v1.1/HG003.bed \
              altair-v1.1 \
              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.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/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

Submitted job 23 with external jobid '4439'.

[Sat May 30 18:16:11 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_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/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
    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_m_giabHC.parse_vcfeval_summary.log
    jobid: 33
    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_m_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/_hg38_m_giabHC/snv_TVBCG5X-HG003-5x-1-D0-PF-CG-MGI_hg38_m_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/_hg38_m_giabHC/summary.txt
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, snv=cgt7p, 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="$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/concordance/_hg38_m_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/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)"

            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_m_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/hg38_m_giabHC/HG003.bed \
              hg38_m_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.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/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

Submitted job 33 with external jobid '4440'.
[Sat May 30 18:16:21 2026]
Finished job 28.
27 of 36 steps (75%) done
Select jobs to execute...

[Sat May 30 18:16:21 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: 27
    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"

            mkdir -p "$(dirname 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)"

            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

Submitted job 27 with external jobid '4441'.
[Sat May 30 18:16:31 2026]
Finished job 25.
28 of 36 steps (78%) done
[Sat May 30 18:16:31 2026]
Finished job 23.
29 of 36 steps (81%) done
[Sat May 30 18:16:41 2026]
Finished job 33.
30 of 36 steps (83%) done
[Sat May 30 18:17:11 2026]
Finished job 27.
31 of 36 steps (86%) done
[Sat May 30 18:17:21 2026]
Finished job 31.
32 of 36 steps (89%) done
Exiting because a job execution failed. Look above for error message

        Womp Womp.  something went awry----
RETURN CODE: 1
[INFO] Workflow exited with status 1
DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260530r48_complete_genomics_mgi_snv_concordance/daylily-omics-analysis$
