DAY-EC activated.
DAY-EC activated.

            outdir="$(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/summary.txt \
              TVBILMN5X-HG003-5x-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" \
              sent \
              dmd \
              sentd \
              > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv
            
Submitted job 17 with external jobid '490'.
[Fri May 29 23:58:57 2026]
Finished job 22.
28 of 36 steps (78%) done
[Fri May 29 23:58:57 2026]
Finished job 13.
29 of 36 steps (81%) done
Select jobs to execute...

[Fri May 29 23:58:57 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.hg38.parse_vcfeval_summary.log
    jobid: 21
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.hg38.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/summary.txt
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, 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="$(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/summary.txt \
              TVBILMN5X-HG003-5x-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" \
              sent \
              dmd \
              sentd \
              > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv
            
Submitted job 21 with external jobid '491'.
[Fri May 29 23:59:07 2026]
Finished job 19.
30 of 36 steps (83%) done
[Fri May 29 23:59:07 2026]
Finished job 15.
31 of 36 steps (86%) done
[Fri May 29 23:59:17 2026]
Finished job 23.
32 of 36 steps (89%) done
[Fri May 29 23:59:47 2026]
Finished job 17.
33 of 36 steps (92%) done
[Fri May 29 23:59:57 2026]
Finished job 21.
34 of 36 steps (94%) done
Select jobs to execute...

[Fri May 29 23:59:57 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fofn, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log
    jobid: 1
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd
    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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.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=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/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/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log;
            
Submitted job 1 with external jobid '492'.
[Sat May 30 00:00:07 2026]
Finished job 1.
35 of 36 steps (97%) done
Select jobs to execute...

[Sat May 30 00:00:07 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 0
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/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=

loading global: /fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
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: ['sentd']
SNV Callers (final): [sentd]
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/ccv20260529r7_illumina_snv_alignstats/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-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:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ'])
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ'])
[Sat May 30 00:00:11 2026]
Finished job 0.
36 of 36 steps (100%) done
Complete log: .snakemake/log/2026-05-29T233850.154429.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 00:03:00,943 INFO Found credentials from IAM Role: dyec-test-RoleHeadNode-eJMKI1vZVQBE
  · Attached export DRA dra-063e210f62c7a3014 at 
/fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/
2026-05-30 00:08:23,342 INFO Task task-0ad201b100ecd9ebe status: PENDING
2026-05-30 00:08:53,529 INFO Task task-0ad201b100ecd9ebe status: EXECUTING
2026-05-30 00:09:23,833 INFO Task task-0ad201b100ecd9ebe status: SUCCEEDED
2026-05-30 00:10:55,736 INFO Wrote export status to /home/ubuntu/daylily-runs/ccv20260529r7_illumina_snv_alignstats/export/fsx_export.yaml

╭────────────────────────────── Export complete ───────────────────────────────╮
│                                                                              │
│  Cluster: dyec-test                                                          │
│  FSx: fs-0df313e1751219cac                                                   │
│  Source: /analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/     │
│  S3:                                                                         │
│  s3://lsmc-ssf-sequencing-data/derived/validation/dyec-test/ubuntu/ccv20260  │
│  529r7_illumina_snv_alignstats/                                              │
│  Status file:                                                                │
│  /home/ubuntu/daylily-runs/ccv20260529r7_illumina_snv_alignstats/export/fsx  │
│  _export.yaml                                                                │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
[INFO] Deleted FSx analysis directory after successful export: /fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats
[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 $::argv0"
      (procedure "cmdModuleAutoinit" line 19)
      invoked from within
  "cmdModuleAutoinit"
      (procedure "module" line 333)
      invoked from within
  "{*}$execcmdlist"
  Please report this issue at https://github.com/cea-hpc/modules/issues
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
DAY-EC activated.
✗ Unexpected error: [Errno 2] No such file or directory
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260529r7_illumina_snv_alignstats/daylily-omics-analysis$
