DAY-EC activated.
DAY-EC activated.
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_clinvar_genes/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/clinvar_genes/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/clinvar_genes/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.clinvar_genes.rtg_vcfeval.log 2>&1
            
Submitted job 19 with external jobid '33'.

[Fri May 29 21:11:59 2026]
rule rtg_vcfeval_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log
    jobid: 21
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=giabHC
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, 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
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log 2>&1
            
Submitted job 21 with external jobid '34'.

[Fri May 29 21:11:59 2026]
rule rtg_vcfeval_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz.tbi, /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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log
    jobid: 27
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=hg38_m_giabHC
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, 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
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log 2>&1
            
Submitted job 27 with external jobid '35'.

[Fri May 29 21:11:59 2026]
rule rtg_vcfeval_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.bed
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC_x_clinvar_genes.rtg_vcfeval.log
    jobid: 23
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC_x_clinvar_genes.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=giabHC_x_clinvar_genes
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, 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
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC_x_clinvar_genes/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC_x_clinvar_genes/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC_x_clinvar_genes.rtg_vcfeval.log 2>&1
            
Submitted job 23 with external jobid '36'.
[Fri May 29 21:11:59 2026]
Finished job 0.
14 of 28 steps (50%) done
[Fri May 29 21:18:20 2026]
Error in rule rtg_vcfeval_roi:
    jobid: 27
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz.tbi, /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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log (check log file(s) for error details)
    conda-env: /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/2dc9c608977f6d7c6253f8d381138ed4_
    shell:
        
            set -euo pipefail
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log 2>&1
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 35

Error executing rule rtg_vcfeval_roi on cluster (jobid: 27, external: 35, jobscript: /fsx/analysis_results/ubuntu/ccv20260529r6_ultima_snv_alignstats/daylily-omics-analysis/.snakemake/tmp.d0f1yyx1/snakejob.rtg_vcfeval_roi.27.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 27.
Select jobs to execute...

[Fri May 29 21:18:20 2026]
rule rtg_vcfeval_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz.tbi, /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/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log
    jobid: 27
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=hg38_m_giabHC
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, 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
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_hg38_m_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/hg38_m_giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.hg38_m_giabHC.rtg_vcfeval.log 2>&1
            
Submitted job 27 with external jobid '99'.
[Fri May 29 21:18:30 2026]
Error in rule rtg_vcfeval_roi:
    jobid: 21
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log (check log file(s) for error details)
    conda-env: /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/2dc9c608977f6d7c6253f8d381138ed4_
    shell:
        
            set -euo pipefail
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log 2>&1
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 34

Error executing rule rtg_vcfeval_roi on cluster (jobid: 21, external: 34, jobscript: /fsx/analysis_results/ubuntu/ccv20260529r6_ultima_snv_alignstats/daylily-omics-analysis/.snakemake/tmp.d0f1yyx1/snakejob.rtg_vcfeval_roi.21.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 21.
Select jobs to execute...

[Fri May 29 21:18:30 2026]
rule rtg_vcfeval_roi:
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed
    output: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt
    log: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log
    jobid: 21
    benchmark: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/benchmarks/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt; Input files updated by another job: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz
    wildcards: sample=TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA, alnr=ug, ddup=na, snv=sentdug, cmpfootprint=giabHC
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, 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
            export TMPDIR="/fsx/scratch/"
            outdir="$(dirname results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/_giabHC/summary.txt)"
            rm -rf "$outdir"

            rtg vcfeval \
              --decompose \
              --squash-ploidy \
              --ref-overlap \
              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.bed \
              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/giabHC/HG003.vcf.gz \
              -c results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/concordance/logs/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.giabHC.rtg_vcfeval.log 2>&1
            
Submitted job 21 with external jobid '100'.
[Fri May 29 21:18:40 2026]
Error in rule rtg_vcfeval_roi:
    jobid: 19
    input: results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentdug/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA.ug.na.sentdug.snv.sort.vcf.gz, results/day/hg38_broad/TVBUG5X-HG003-5x-1-D0-PF-UG-ULTIMA/align/ug/na/snv/sentd--output truncated--
