DAY-EC activated.
DAY-EC activated.
## session ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun
## repo /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
## run_dir /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun
## sentinel files
1780127720.0000000000 1323 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/unlock_fails.log
1780127718.0000000000 444 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/logs/about.log
1780127712.0000000000 833 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/day_cmd.log
## run state files
1780127720.1164409300 703721 /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/tmux.log
1780127717.7294409950 872 /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/status.json
1780127544.6474465380 0 /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/tmux-bootstrap.log
1780127544.6464465380 28098 /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/launch.sh
## command wrapper logs
### /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/status.json
{
  "command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'ht
  "completed_at": "2026-05-30T07:55:17Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis",
  "session_name": "ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun",
  "started_at": "2026-05-30T07:52:26Z"
}
### /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/tmux.log
        else
            vep             --dir_cache /fsx/references/runtime_assets/tool_specific_resources/vep/             --offline             --vcf             --cache             --cache_version 114             --input_file results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz             --chr chr19
        fi
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.log 2>&1
        cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.input.vcf.gz.record_count > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz.record_count
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz.tbi


[Sat May 30 07:55:17 2026]
rule vep_chromosome:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-P
    output: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-I
    log: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.log
    jobid: 96
    benchmark: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/benchmarks/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.bench.tsv
    reason: Missing output files: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.record_count; Input files u
    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr11
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i128, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz) $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.log)
        test -d /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38 || (
            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
            exit 2
        )
        records=$(cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.record_count)
        if [ "$records" -eq 0 ]; then
            gzip -cd results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz | awk '/^#/' | bgzip -c > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz
        else
            vep             --dir_cache /fsx/references/runtime_assets/tool_specific_resources/vep/             --offline             --vcf             --cache             --cache_version 114             --input_file results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz             --chr chr11
        fi
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.log 2>&1
        cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.input.vcf.gz.record_count > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.record_count
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.tbi


[Sat May 30 07:55:17 2026]
rule vep_chromosome:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-IL
    output: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-
    log: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.log
    jobid: 78
    benchmark: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/benchmarks/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.bench.tsv
    reason: Missing output files: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.record_count, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.tbi; Input files updat
    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr2
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i128, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz) $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.log)
        test -d /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38 || (
            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
            exit 2
        )
        records=$(cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz.record_count)
        if [ "$records" -eq 0 ]; then
            gzip -cd results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz | awk '/^#/' | bgzip -c > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz
        else
            vep             --dir_cache /fsx/references/runtime_assets/tool_specific_resources/vep/             --offline             --vcf             --cache             --cache_version 114             --input_file results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz             --chr chr2
        fi
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.log 2>&1
        cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.input.vcf.gz.record_count > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.record_count
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.tbi


[Sat May 30 07:55:17 2026]
rule vep_chromosome:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-IL
    output: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-
    log: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.log
    jobid: 88
    benchmark: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/benchmarks/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.bench.tsv
    reason: Missing output files: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.record_count; Input files updat
    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr7
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i128, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz) $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.log)
        test -d /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38 || (
            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
            exit 2
        )
        records=$(cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz.record_count)
        if [ "$records" -eq 0 ]; then
            gzip -cd results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz | awk '/^#/' | bgzip -c > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz
        else
            vep             --dir_cache /fsx/references/runtime_assets/tool_specific_resources/vep/             --offline             --vcf             --cache             --cache_version 114             --input_file results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz             --chr chr7
        fi
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.log 2>&1
        cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.input.vcf.gz.record_count > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.record_count
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.tbi


[Sat May 30 07:55:17 2026]
rule vep_chromosome:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-P
    output: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-I
    log: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.log
    jobid: 116
    benchmark: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/benchmarks/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.bench.tsv
    reason: Missing output files: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.record_count, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.tbi; Input files u
    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd, vepchrm=chr21
    threads: 16
    resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i128, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz) $(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.log)
        test -d /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38 || (
            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
            exit 2
        )
        records=$(cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz.record_count)
        if [ "$records" -eq 0 ]; then
            gzip -cd results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz | awk '/^#/' | bgzip -c > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz
        else
            vep             --dir_cache /fsx/references/runtime_assets/tool_specific_resources/vep/             --offline             --vcf             --cache             --cache_version 114             --input_file results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz             --chr chr21
        fi
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.log 2>&1
        cat results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.input.vcf.gz.record_count > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.record_count
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.tbi


[Sat May 30 07:55:17 2026]
rule vep_chromosome:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.--output truncated--