DAY-EC activated.
DAY-EC activated.
7 of 15 steps (47%) done
[Sat May 30 15:50:19 2026]
Finished job 10.
8 of 15 steps (53%) done
[Sat May 30 15:53:39 2026]
Finished job 8.
9 of 15 steps (60%) done
Select jobs to execute...

[Sat May 30 15:53:39 2026]
rule run_bclconvert:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L001/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L002/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L004/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L005/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L006/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L007/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L008/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L001/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L002/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L004/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L005/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L006/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L007/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L008/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L001/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L002/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L004/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L005/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L006/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L007/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L008/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L001/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L002/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L004/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L005/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L006/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L007/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L008/SampleSheet.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.merge_lanes.log
    jobid: 2
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.merge_lanes.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L007/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L004/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L001/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L002/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L007/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L008/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L002/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L008/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L005/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L008/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L002/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L004/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L002/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L006/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L005/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L006/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L006/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L007/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L005/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L006/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L004/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L007/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L004/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L005/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L008/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L001/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L001/SampleSheet.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L001/bclconvert.done
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

python workflow/scripts/dyec_merge_bclconvert_lanes.py --lane-fastq-root results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs --final-fastq-dir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs --report-dir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports --lanes L001,L002,L003,L004,L005,L006,L007,L008 --done results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done --log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.merge_lanes.log >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.merge_lanes.log 2>&1 && test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv && test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv
Submitted job 2 with external jobid '3545'.
[Sat May 30 15:59:48 2026]
Finished job 2.
10 of 15 steps (67%) done
Select jobs to execute...

[Sat May 30 15:59:48 2026]
rule bclconvert_metrics_summary:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log
    jobid: 12
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_metrics_summary.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log
        python workflow/scripts/bclconvert_metrics_summary.py \
          --report-dir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports \
          --demux-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv \
          --unknown-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv \
          --hopping-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv \
          --fastq-manifest-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv \
          --rollup-json-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log 2>&1

Submitted job 12 with external jobid '3546'.

[Sat May 30 15:59:48 2026]
rule bclconvert_generate_units_tsv:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log
    jobid: 11
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_generate_units_tsv.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log
        seq_platform_override=
        python workflow/scripts/bclconvert_fastq_list_to_units.py \
          --fastq-list results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv \
          --sample-sheet-rows results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv \
          --run-id 20260514_LH01106_0009_B23TVLGLT4 \
          --libprep PCR-FREE \
          --seq-vendor ILMN \
          --seq-platform-override "$seq_platform_override" \
          --units-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log 2>&1

Submitted job 11 with external jobid '3547'.
[Sat May 30 16:03:59 2026]
Error in rule bclconvert_metrics_summary:
    jobid: 12
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log (check log file(s) for error details)
    conda-env: /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/829d8a014f8720620c5866151c8f0779_
    shell:

        set -euo pipefail
        mkdir -p results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log
        python workflow/scripts/bclconvert_metrics_summary.py \
          --report-dir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports \
          --demux-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv \
          --unknown-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv \
          --hopping-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv \
          --fastq-manifest-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv \
          --rollup-json-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log 2>&1

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 3546

Error executing rule bclconvert_metrics_summary on cluster (jobid: 12, external: 3546, jobscript: /fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/.snakemake/tmp.75tr6v54/snakejob.bclconvert_metrics_summary.12.sh). For error details see the cluster log and the log files of the involved rule(s).
[Sat May 30 16:03:59 2026]
Error in rule bclconvert_generate_units_tsv:
    jobid: 11
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log (check log file(s) for error details)
    conda-env: /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/829d8a014f8720620c5866151c8f0779_
    shell:

        set -euo pipefail
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log
        seq_platform_override=
        python workflow/scripts/bclconvert_fastq_list_to_units.py \
          --fastq-list results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv \
          --sample-sheet-rows results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv \
          --run-id 20260514_LH01106_0009_B23TVLGLT4 \
          --libprep PCR-FREE \
          --seq-vendor ILMN \
          --seq-platform-override "$seq_platform_override" \
          --units-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log 2>&1

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 3547

Error executing rule bclconvert_generate_units_tsv on cluster (jobid: 11, external: 3547, jobscript: /fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/.snakemake/tmp.75tr6v54/snakejob.bclconvert_generate_units_tsv.11.sh). For error details see the cluster log and the log files of the involved rule(s).
Trying to restart job 12.
Select jobs to execute...

[Sat May 30 16:03:59 2026]
rule bclconvert_metrics_summary:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log
    jobid: 12
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_metrics_summary.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        mkdir -p results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log
        python workflow/scripts/bclconvert_metrics_summary.py \
          --report-dir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports \
          --demux-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv \
          --unknown-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv \
          --hopping-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv \
          --fastq-manifest-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv \
          --rollup-json-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_metrics_summary.log 2>&1

Submitted job 12 with external jobid '3548'.
Trying to restart job 11.
Select jobs to execute...

[Sat May 30 16:03:59 2026]
rule bclconvert_generate_units_tsv:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log
    jobid: 11
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_generate_units_tsv.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        set -euo pipefail
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_tsv.log
        seq_platform_override=
        python workflow/scripts/bclconvert_fastq_list_to_units.py \
          --fastq-list results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv \
          --sample-sheet-rows results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv \
          --run-id 20260514_LH01106_0009_B23TVLGLT4 \
          --libprep PCR-FREE \
          --seq-vendor ILMN \
          --seq-platform-override "$seq_platform_override" \
          --units-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_generate_units_ts--output truncated--
