DAY-EC activated.
DAY-EC activated.
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
Creating conda environment workflow/envs/bclconvert_metrics_v0.1.yaml...
Downloading and installing remote packages.
Environment for /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/workflow/rules/../envs/bclconvert_metrics_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-225/841ac27cc5e7759e4ad9d0f5f4e02ac4_)
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cluster nodes: 192
Job stats:
job                           count    min threads    max threads
--------------------------  -------  -------------  -------------
bclconvert_validate_inputs        1              1              1
produce_bclconvert_fastqs         1              1              1
run_bclconvert                    1              1              1
run_bclconvert_lane               1            192            192
total                             4              1            192

Select jobs to execute...

[Tue Jun  2 00:11:10 2026]
localrule bclconvert_validate_inputs:
    input: /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv, /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/samples.tsv
    output: 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/tables/samplesheet_rows.tsv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
    jobid: 1
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_validate_inputs.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    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
        mkdir -p results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables
        : > results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
        if [ -z /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir is required" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ ! -d /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 ]; then
            echo "bclconvert.run_dir does not exist: /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        if [ "true" = "false" ]; then
            echo "keep_undetermined_fastqs=false is unsupported for the bclconvert bootstrap path" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        bcl_extra_args=
        if [ -n "$bcl_extra_args" ]; then
            echo "bclconvert.extra_args is not supported in this shell-only bootstrap workflow" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
            exit 2
        fi
        python workflow/scripts/parse_bclconvert_samplesheet.py \
          --sample-sheet /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv \
          --samples-tsv /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/samples.tsv \
          --normalized-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv \
          --rows-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv \
          --runtime-version 4.0.3 \
          --sampleproject-subdirectories false \
          --warnings-out results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.warnings.log \
          >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log 2>&1
        touch results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok
        
Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-225/841ac27cc5e7759e4ad9d0f5f4e02ac4_
[Tue Jun  2 00:11:11 2026]
Finished job 1.
1 of 4 steps (25%) done
Select jobs to execute...

[Tue Jun  2 00:11:11 2026]
rule run_bclconvert_lane:
    input: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    output: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/SampleSheet.csv
    log: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.log
    jobid: 3
    benchmark: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/run_bclconvert.L003.bench.tsv
    reason: Missing output files: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/SampleSheet.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; Input files updated by another job: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
    wildcards: lane=L003
    threads: 192
    resources: mem_mb=360000, mem_mib=343323, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=192, time=5440, partition=i192mem, vcpu=192, distribution=block, exclusive=--exclusive, constraint=, exclude=, include=

TMPDIR=/dev/shm bash workflow/scripts/run_bclconvert_lane.sh docker://nfcore/bclconvert:4.0.3 /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000733Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv 3 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/SampleSheet.csv false false false 1 24 4 64 32 true true 1000 '{"BarcodeMismatchesIndex1": "0", "BarcodeMismatchesIndex2": "0"}' '{}' -f 192 results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.L003.log results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/fastq_list.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_fastqs/L003/Reports/Demultiplex_Stats.csv results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/lane_reports/L003/bclconvert.done ""
Submitted job 3 with external jobid '1'.
