DAY-EC activated.
DAY-EC activated.
            # 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
            
Submitted job 750 with external jobid '2641'.
[Sat May 30 01:58:01 2026]
Finished job 747.
755 of 763 steps (99%) done
Select jobs to execute...

[Sat May 30 01:58:01 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/_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/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
    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.giabHC.parse_vcfeval_summary.log
    jobid: 746
    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.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/_giabHC/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_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/_giabHC/summary.txt
    wildcards: sample=TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd, snv=sentdhiomr, 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="$(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/concordance/_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/giabHC/HG003.bed \
              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.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
            
Submitted job 746 with external jobid '2642'.
[Sat May 30 01:58:01 2026]
Finished job 742.
756 of 763 steps (99%) done
[Sat May 30 01:58:11 2026]
Finished job 744.
757 of 763 steps (99%) done
[Sat May 30 01:58:11 2026]
Finished job 748.
758 of 763 steps (99%) done
[Sat May 30 01:58:21 2026]
Finished job 752.
759 of 763 steps (99%) done
[Sat May 30 01:59:12 2026]
Finished job 746.
760 of 763 steps (99.6%) done
[Sat May 30 01:59:22 2026]
Finished job 750.
761 of 763 steps (99.7%) done
Select jobs to execute...

[Sat May 30 01:59:22 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: 19
    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/_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/_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/_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/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/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/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/_giabHC_x_clinvar_genes/snv_TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv
    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;
            
Submitted job 19 with external jobid '2643'.
[Sat May 30 01:59:32 2026]
Finished job 19.
762 of 763 steps (99.9%) done
Select jobs to execute...

[Sat May 30 01:59:32 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: 18
    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/_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/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/_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_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/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=

Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/daylily-omics-analysis/config/global_AWSPC.yaml
Config file config/global_AWSPC.yaml is extended by additional config specified via the command line.
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
Config file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.
INFO::: The genome build hg38_broad is supported.  The genome build prefix is 'chr''.
...WARNING: No aligners set in the config.
...INFO: Auto-detected aligners from env: ['sent']
aligners (final): [sent]
...INFO: No dedupers set in config. Defaulting to na (no dedup).
...INFO: Auto-detected dedupers. DDUP updated to: ['dmd']
deduper (final): [dmd]
...WARNING: No snv_callers set in the config.
...INFO: Auto-detected SNV callers from env: ['sentdhiomr']
SNV Callers (final): [sentdhiomr]
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentdhiomr']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ': ['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ'])
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, threads=1, time=5440, vcpu=1
Select jobs to execute...
All Wildcards:    all snv_CALLERS:  ['sentdhiomr']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ': ['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ'])
All Wildcards:    all snv_CALLERS:  ['sentdhiomr']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ': ['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ'])
[Sat May 30 01:59:35 2026]
Finished job 18.
763 of 763 steps (100%) done
Complete log: .snakemake/log/2026-05-30T010427.416050.snakemake.log


	WARNING!!!! ALL Directories Are Remaining Unlocked. To have directories lock automatically upon successful completion, set --lock-analysis-dirs when calling day-run.


 
]]]]--------WORKFLOW SUCCESS====================]]]]]--
RETURN CODE: 0
⚠ Active conda environment is 'DAYOA', not DAY-EC. Continuing anyway; the 
supported path is `source ./activate`.

── EXPORT ──
  › Preparing direct FSx export DRA
2026-05-30 01:59:47,115 INFO Found credentials from IAM Role: dyec-test-RoleHeadNode-eJMKI1vZVQBE
  · Attached export DRA dra-02b688cfbfab95995 at 
/fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/
2026-05-30 02:02:53,430 INFO Task task-0bfc5c815748799e2 status: PENDING
2026-05-30 02:03:23,775 INFO Task task-0bfc5c815748799e2 status: EXECUTING
2026-05-30 02:03:54,028 INFO Task task-0bfc5c815748799e2 status: EXECUTING
2026-05-30 02:04:24,345 INFO Task task-0bfc5c815748799e2 status: SUCCEEDED
2026-05-30 02:04:40,041 INFO Wrote export status to /home/ubuntu/daylily-runs/ccv20260529r10_inflection-bjuice-product-v0.1/export/fsx_export.yaml

╭────────────────────────────── Export complete ───────────────────────────────╮
│                                                                              │
│  Cluster: dyec-test                                                          │
│  FSx: fs-0df313e1751219cac                                                   │
│  Source:                                                                     │
│  /analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1/     │
│  S3:                                                                         │
│  s3://lsmc-ssf-sequencing-data/derived/validation/dyec-test/ubuntu/ccv20260  │
│  529r10_inflection-bjuice-product-v0.1/                                      │
│  Status file:                                                                │
│  /home/ubuntu/daylily-runs/ccv20260529r10_inflection-bjuice-product-v0.1/ex  │
│  port/fsx_export.yaml                                                        │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
[INFO] Deleted FSx analysis directory after successful export: /fsx/analysis_results/ubuntu/ccv20260529r10_inflection-bjuice-product-v0.1
[INFO] Workflow exited with status 0
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
ERROR: error getting working directory name: no such file or directory
      while executing
  "pwd"
      (procedure "getAbsolutePath" line 9)
      invoked from within
  "getAbsolutePath $::argv0"
      (procedure "cmdModuleAutoinit" line 19)
      invoked from --output truncated--
