DAY-EC activated.
DAY-EC activated.

Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/829d8a014f8720620c5866151c8f0779_
[Sat May 30 23:25:23 2026]
Finished job 17.
16 of 21 steps (76%) done
[Sat May 30 23:25:24 2026]
Finished job 18.
17 of 21 steps (81%) done
Select jobs to execute...

[Sat May 30 23:25:24 2026]
rule bclconvert_metrics_multiqc_exports:
    input: 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
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_demux_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_unknown_barcodes_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_index_hopping_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_fastq_manifest_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_lane_summary_mqc.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/logs/bclconvert_metrics_multiqc_exports.log
    jobid: 19
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_metrics_multiqc_exports.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done; Input files updated by another job: 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/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json
    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/multiqc_inputs results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/logs
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/logs/bclconvert_metrics_multiqc_exports.log
        python workflow/scripts/bclconvert_metrics_to_multiqc.py \
          --demux-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv \
          --unknown-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv \
          --hopping-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv \
          --fastq-manifest-tsv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv \
          --rollup-json results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json \
          --demux-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_demux_mqc.tsv \
          --unknown-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_unknown_barcodes_mqc.tsv \
          --hopping-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_inputs/bclconvert_index_hopping_mqc.tsv \
          --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

Submitted job 19 with external jobid '4661'.
[Sat May 30 23:30:09 2026]
Finished job 19.
18 of 21 steps (86%) done
Select jobs to execute...

[Sat May 30 23:30:09 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/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
    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

Submitted job 20 with external jobid '4662'.
[Sat May 30 23:31:29 2026]
Finished job 20.
19 of 21 steps (90%) done
Select jobs to execute...

[Sat May 30 23:31:29 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/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.html, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/rollup.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.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
Touching output file results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete.
[Sat May 30 23:31:29 2026]
Finished job 6.
20 of 21 steps (95%) done
Select jobs to execute...

[Sat May 30 23:31:29 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/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
    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=

[Sat May 30 23:31:29 2026]
Finished job 0.
21 of 21 steps (100%) done
