DAY-EC activated.
DAY-EC activated.
            exit $cli_rc;
        fi

        # --- Reheader SNV VCF: rename sample to cluster_sample ---
        if [ -f "${cli_out}.vcf.gz" ]; then
            oldname=$(bcftools query -l "${cli_out}.vcf.gz" | head -n1);
            echo -e "${oldname}	TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION" > "$TMPDIR/rename.txt";
            bcftools reheader -s "$TMPDIR/rename.txt" -o 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 "${cli_out}.vcf.gz" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o 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/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/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
        else
            echo "ERROR: SNV VCF not produced by sentieon-cli" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
            exit 20;
        fi

        # --- Reheader SV VCF ---
        if [ -f "${cli_out}.sv.vcf.gz" ]; then
            bcftools reheader -s "$TMPDIR/rename.txt" -o 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.sv.vcf.gz "${cli_out}.sv.vcf.gz" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o 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.sv.vcf.gz.tbi 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.sv.vcf.gz >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
        else
            echo "WARNING: SV VCF not produced; creating empty placeholder" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
            touch 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.sv.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.sv.vcf.gz.tbi;
        fi

        end_time=$(date +%s);
        elapsed_time=$((($end_time - $start_time) / 60));
        echo "Elapsed-Time-min:	$itype	$elapsed_time" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;


Submitted job 1 with external jobid '119'.

[Fri May 29 21:25:05 2026]
rule no_dedup_cram:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram.crai
    output: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai
    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log
    jobid: 8
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mrkdup.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram.crai, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont
    priority: 3
    resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192, vcpu=1, 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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram)
        touch results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log

        # Use relative symlinks so the tree is relocatable
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram) results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram)" results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log 2>&1
        ln -sfn "$(realpath --relative-to=$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai) results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram.crai)" results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log 2>&1

        echo "Symlinked results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram → results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log 2>&1
        echo "Symlinked results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.cram.crai → results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/logs/dedupe.na.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.log 2>&1

Submitted job 8 with external jobid '120'.
[Fri May 29 21:25:15 2026]
Finished job 8.
2 of 23 steps (9%) done
Select jobs to execute...

[Fri May 29 21:25:15 2026]
rule alignstats:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai
    output: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.json
    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.log
    jobid: 7
    benchmark: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/benchmarks/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.json; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram.crai, results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na
    threads: 96
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=96, time=5440, partition=i192,i192mem,i128, vcpu=96, distribution=block, exclusive=, constraint=, exclude=, include=, attempt_n=1

resources/alignstats/alignstats  -C -U  -i results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.cram -T /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -o results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.json  -j cram -v -P 96 -p 96 > results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.log;
Submitted job 7 with external jobid '121'.
[Fri May 29 21:26:15 2026]
Finished job 7.
3 of 23 steps (13%) done
Select jobs to execute...

[Fri May 29 21:26:15 2026]
localrule finish_align_stats:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.json
    output: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.tsv
    jobid: 6
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.json
    wildcards: sample=TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION, alnr=ont, ddup=na
    threads: 2
    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...
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...
[Fri May 29 21:26:18 2026]
Finished job 6.
4 of 23 steps (17%) done
Select jobs to execute...

[Fri May 29 21:26:18 2026]
localrule alignstats_gather:
    input: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.tsv
    output: results/day/hg38_broad/other_reports/alignstats_summary_gather.done, results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_gather.log
    jobid: 5
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_summary_gather.done; Input files updated by another job: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/alignstats/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.alignstats.tsv
    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=

 touch results/day/hg38_broad/other_reports/alignstats_summary_gather.done; touch results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/e28353b323f26af0747eb0fc4db2c579_
[Fri May 29 21:26:19 2026]
Finished job 5.
5 of 23 steps (22%) done
Select jobs to execute...

[Fri May 29 21:26:19 2026]
localrule alignstats_compile:
    input: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    output: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv, results/day/hg38_broad/other_reports/alignstats_csummary.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_compile.log
    jobid: 4
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_smmary_compile.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv; Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    threads: 2
    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=


        set -euo pipefail
        python workflow/scripts/compile_alignstats.py           --mdir results/day/hg38_broad/           --log results/day/hg38_broad/logs/alignstats_summary_compile.log           --bsummary results/day/hg38_broad/other_reports/alignstats_bsummary.tsv           --csummary results/day/hg38_broad/other_reports/alignstats_csummary.tsv           --combo results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv           --generalstats results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv

[Fri May 29 21:26:19 2026]
Finished job 4.
6 of 23 steps (26%) done
Removing temporary output results/day/hg38_broad/other_reports/alignstats_csummary.tsv.
Select jobs to execute...

[Fri May 29 21:26:19 2026]
localrule produce_alignstats:
    input: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    jobid: 3
    reason: Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    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=

[Fri May 29 21:26:19 2026]
Finished job 3.
7 of 23 steps (30%) done
Removing temporary output results/day/hg38_broad/other_reports/alignstats_bsummary.tsv.
[Fri May 29 21:38:26 2026]
Finished job 1.
8 of 23 steps (35%) done
Select jobs to execute...

[Fri May 29 21:38:26 2026]
rule rtg_vcfeval_roi:
    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, /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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/summary.txt
    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.giabHC.rtg_vcfeval.log
    jobid: 16
    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.giabHC.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/summary.txt; 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, 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, 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="$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC/summary.txt)"
            rm -rf "$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/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 \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > 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.giabHC.rtg_vcfeval.log 2>&1

Submitted job 16 with external jobid '122'.

[Fri May 29 21:38:26 2026]
rule rtg_vcfeval_roi:
    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, /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/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/summary.txt
    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.giabHC_x_clinvar_genes.rtg_vcfeval.log
    jobid: 18
    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.giabHC_x_clinvar_genes.rtg_vcfeval.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/summary.txt; 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, 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, 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="$(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_giabHC_x_clinvar_genes/summary.txt)"
            rm -rf "$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/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 \
              -o "$outdir" \
              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.sdf \
              --threads 16 \
              > 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.giabHC_x_clinvar_genes.rtg_vcfeval.log 2>&1

Submitted job 18 with external jobid '123'.

[Fri May 29--output truncated--
