DAY-EC activated.
DAY-EC activated.
    jobid: 13
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.clinvar_genes.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/summary.txt
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na, snv=sentdont, 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="$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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"

            python workflow/scripts/parse-vcfeval-summary.py \
              results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/summary.txt \
              TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION \
              /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" \
              ont \
              na \
              sentdont \
              > results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv
            
Submitted job 13 with external jobid '133'.
[Fri May 29 21:40:07 2026]
Finished job 17.
15 of 23 steps (65%) done
Select jobs to execute...

[Fri May 29 21:40:07 2026]
localrule produce_sentdont_snv_vcf:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz.tbi
    output: results/day/hg38_broad/logs/target_aliases/produce_sentdont_snv_vcf.done
    jobid: 0
    reason: Missing output files: results/day/hg38_broad/logs/target_aliases/produce_sentdont_snv_vcf.done; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz.tbi
    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=

mkdir -p $(dirname results/day/hg38_broad/logs/target_aliases/produce_sentdont_snv_vcf.done); touch results/day/hg38_broad/logs/target_aliases/produce_sentdont_snv_vcf.done;
[Fri May 29 21:40:07 2026]
Finished job 0.
16 of 23 steps (70%) done
[Fri May 29 21:40:17 2026]
Finished job 21.
17 of 23 steps (74%) done
[Fri May 29 21:40:27 2026]
Finished job 13.
18 of 23 steps (78%) done
[Fri May 29 21:40:47 2026]
Finished job 15.
19 of 23 steps (83%) done
[Fri May 29 21:41:07 2026]
Finished job 20.
20 of 23 steps (87%) done
Select jobs to execute...

[Fri May 29 21:41:07 2026]
rule parse_vcfeval_summary_roi:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv
    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.hg38.parse_vcfeval_summary.log
    jobid: 19
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.hg38.parse_vcfeval_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/summary.txt
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na, snv=sentdont, 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="$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/summary.txt)"
            # This file is legacy/debug; parse-vcfeval-summary.py uses its dirname to place the MQC TSV.
            legacy_parsed="$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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/summary.txt \
              TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION \
              /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 \
              na \
              sentdont \
              > results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv
            
Submitted job 19 with external jobid '134'.
[Fri May 29 21:42:07 2026]
Finished job 19.
21 of 23 steps (91%) done
Select jobs to execute...

[Fri May 29 21:42:07 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1.1/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38_m_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.done, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.fofn, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.concordance.log
    jobid: 10
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38_m_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1.1/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.sort.vcf.gz
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na, snv=sentdont
    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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.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=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1.1/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38_m_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.concordance.log;
            
Submitted job 10 with external jobid '135'.
[Fri May 29 21:42:17 2026]
Finished job 10.
22 of 23 steps (96%) done
Select jobs to execute...

[Fri May 29 21:42:17 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.done, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1.1/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38_m_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38_m_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_hg38/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1.1/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/concordance.done, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/snv_TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION_giabHC_x_clinvar_genes_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=

loading global: /fsx/analysis_results/ubuntu/ccv20260529r6_ont_snv_alignstats/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r6_ont_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.
aligners (final): []
...INFO: No dedupers set in config. Defaulting to na (no dedup).
deduper (final): [na]
...WARNING: No snv_callers set in the config.
...INFO: Auto-detected SNV callers from env: ['sentdont']
SNV Callers (final): [sentdont]
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/ccv20260529r6_ont_snv_alignstats/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r6_ont_snv_alignstats/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentdont']  all ALIGNERS:  []  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION': ['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION']}  all concordance samples:  dict_keys(['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION'])
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:  ['sentdont']  all ALIGNERS:  []  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION': ['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION']}  all concordance samples:  dict_keys(['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION'])
All Wildcards:    all snv_CALLERS:  ['sentdont']  all ALIGNERS:  []  all CRAM_ALIGNERS:  ['ont']  all samples:  {'TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION': ['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION']}  all concordance samples:  dict_keys(['TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION'])
[Fri May 29 21:42:20 2026]
Finished job 9.
23 of 23 steps (100%) done
Complete log: .snakemake/log/2026-05-29T212317.185118.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
2026-05-29 21:42:30,136 INFO Found credentials from IAM Role: dyec-test-RoleHeadNode-eJMKI1vZVQBE
2026-05-29 21:42:30,245 ERROR FSx export failed: Unable to inspect S3 destination prefix s3://lsmc-dayoa-analysis-results-usw2/validation/dyec-test/ubuntu/ccv20260529r6_ont_snv_alignstats/: An error occurred (AccessDenied) when calling the ListObjectsV2 operation: User: arn:aws:sts::108782052779:assumed-role/dyec-test-RoleHeadNode-eJMKI1vZVQBE/i-0cac5db332e3c70e5 is not authorized to perform: s3:ListBucket on resource: "arn:aws:s3:::lsmc-dayoa-analysis-results-usw2" because no identity-based policy allows the s3:ListBucket action
2026-05-29 21:42:30,250 INFO Wrote export status to /home/ubuntu/daylily-runs/ccv20260529r6_ont_snv_alignstats/export/fsx_export.yaml

╭─────────────────────────────── Export failed ────────────────────────────────╮
│                                                                              │
│  Unable to inspect S3 destination prefix                                     │
│  s3://lsmc-dayoa-analysis-results-usw2/validation/dyec-test/ubuntu/ccv20260  │
│  529r6_ont_snv_alignstats/: An error occurred (AccessDenied) when calling    │
│  the ListObjectsV2 operation: User:                                          │
│  arn:aws:sts::108782052779:assumed-role/dyec-test-RoleHeadNode-eJMKI1vZVQBE  │
│  /i-0cac5db332e3c70e5 is not authorized to perform: s3:ListBucket on         │
│  resource: "arn:aws:s3:::lsmc-dayoa-analysis-results-usw2" because no        │
│  identity-based policy allows the s3:ListBucket action                       │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
[ERROR] Export failed with status 1
[INFO] Workflow exited with status 1
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubu--output truncated--
