DAY-EC activated.
DAY-EC activated.
          --fastq-manifest-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_fastq_manifest_mqc.tsv \
          --lane-summary-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_lane_summary_mqc.tsv \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/logs/bclconvert_metrics_multiqc_exports.log 2>&1


[Sat May 30 21:51:58 2026]
rule multiqc_bclconvert:
    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, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/multiqc_bclconvert.log
    jobid: 20
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/multiqc_bclconvert.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done
    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
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/multiqc_bclconvert.log
        multiqc -f \
          -m bclconvert \
          -m custom_content \
          --config config/external_tools/multiqc_config.yaml \
          --template default \
          --filename multiqc_report.html \
          --outdir results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert \
          results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports \
          results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/multiqc_bclconvert.log 2>&1
        test -s results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html


[Sat May 30 21:51:58 2026]
localrule produce_bclconvert_fastqs_and_metrics:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv, 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, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete
    jobid: 6
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, 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/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.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/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete

[Sat May 30 21:51:58 2026]
localrule produce_illumina_run_qc_and_bclconvert:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete
    jobid: 0
    reason: Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/multiqc_report.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/run_qc/illumina/summary.html
    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=

Job stats:
job                                       count    min threads    max threads
--------------------------------------  -------  -------------  -------------
bclconvert_generate_units_tsv                 1              1              1
bclconvert_metrics_multiqc_exports            1              1              1
bclconvert_metrics_summary                    1              1              1
bclconvert_validate_inputs                    1              1              1
illumina_run_qc_fetch_metric_subset           1              1              1
illumina_run_qc_interop_summary               1              1              1
illumina_run_qc_json                          1              1              1
illumina_run_qc_multiqc                       1              1              1
illumina_run_qc_report                        1              1              1
multiqc_bclconvert                            1              1              1
produce_bclconvert_fastqs_and_metrics         1              1              1
produce_illumina_run_qc_and_bclconvert        1              1              1
run_bclconvert                                1              1              1
run_bclconvert_lane                           8            192            192
total                                        21              1            192

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        bclconvert_generate_units_tsv, bclconvert_metrics_multiqc_exports, bclconvert_metrics_summary, illumina_run_qc_interop_summary, illumina_run_qc_json, illumina_run_qc_multiqc, illumina_run_qc_report, multiqc_bclconvert, produce_bclconvert_fastqs_and_metrics, produce_illumina_run_qc_and_bclconvert, run_bclconvert, run_bclconvert_lane
    missing output files:
        bclconvert_generate_units_tsv, bclconvert_metrics_multiqc_exports, bclconvert_metrics_summary, bclconvert_validate_inputs, illumina_run_qc_fetch_metric_subset, illumina_run_qc_interop_summary, illumina_run_qc_json, illumina_run_qc_multiqc, illumina_run_qc_report, multiqc_bclconvert, produce_bclconvert_fastqs_and_metrics, run_bclconvert, run_bclconvert_lane

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
RETURN CODE: 0
[INFO] Workflow exited with status 0
DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260530r57_illumina_run_qc_bclconvert_dryrun/daylily-omics-analysis$
