DAY-EC activated.
DAY-EC activated.
                fi
                echo "Staging BCL run directory from S3 to scratch: $(date -Is)" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "s3_stage_lanes: $(printf "%s" "$lane_ids" | tr '\n' ' ')" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                if ! AWS_REGION="$run_region" AWS_DEFAULT_REGION="$run_region" AWS_MAX_ATTEMPTS=10 AWS_RETRY_MODE=adaptive \
                  aws s3 sync "$run_uri/" "$scratch_run_dir/" \
                    --exclude "Analysis/*" \
                    --exclude "Data/Intensities/BaseCalls/L*/*" \
                    --only-show-errors \
                    > "$scratch_sync_log_dir/root.log" 2>&1; then
                    cat "$scratch_sync_log_dir/root.log" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    echo "Root-level aws s3 sync failed" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                pids=()
                for lane_id in $lane_ids; do
                    (
                        AWS_REGION="$run_region" AWS_DEFAULT_REGION="$run_region" AWS_MAX_ATTEMPTS=10 AWS_RETRY_MODE=adaptive \
                          aws s3 sync "$run_uri/Data/Intensities/BaseCalls/$lane_id/" "$scratch_run_dir/Data/Intensities/BaseCalls/$lane_id/" \
                            --only-show-errors
                    ) > "$scratch_sync_log_dir/$lane_id.log" 2>&1 &
                    pids+=("$!")
                done
                sync_rc=0
                for pid in "${pids[@]}"; do
                    if ! wait "$pid"; then
                        sync_rc=1
                    fi
                done
                cat "$scratch_sync_log_dir"/*.log >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                if [ "$sync_rc" -ne 0 ]; then
                    echo "One or more lane-level aws s3 sync processes failed" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                echo "S3 scratch staging complete: $(date -Is)" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                du -sh "$scratch_run_dir" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log 2>&1 || true
                effective_run_dir="$scratch_run_dir"
                effective_output_dir="$scratch_output_dir"
                df -h "$scratch_root" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log 2>&1 || true
                ;;
            *)
                echo "Unsupported bclconvert.staging_mode: $staging_mode" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                exit 2
                ;;
        esac

        parallel_tiles=8
        conversion_threads=8
        compression_threads=12
        decompression_threads=4
        per_tile_threads="$((conversion_threads + compression_threads + decompression_threads))"
        if [ "$per_tile_threads" -lt 1 ]; then
            echo "BCLConvert per-tile thread total must be >= 1" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
            exit 2
        fi
        max_parallel_tiles="$((192 / per_tile_threads))"
        if [ "$max_parallel_tiles" -lt 1 ]; then
            echo "BCLConvert thread allocation is too small: threads=192 per_tile_threads=$per_tile_threads" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
            exit 2
        fi
        if [ "$parallel_tiles" -gt "$max_parallel_tiles" ]; then
            echo "Reducing BCLConvert parallel tiles from $parallel_tiles to $max_parallel_tiles for threads=192" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
            parallel_tiles="$max_parallel_tiles"
        fi
        echo "bcl_num_parallel_tiles: $parallel_tiles" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        echo "bcl_num_conversion_threads: $conversion_threads" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        echo "bcl_num_compression_threads: $compression_threads" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        echo "bcl_num_decompression_threads: $decompression_threads" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log

        bcl_flags=(
          --bcl-input-directory "$effective_run_dir"
          --output-directory "$effective_output_dir"
          --sample-sheet results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
          --strict-mode false
          --first-tile-only false
          --bcl-sampleproject-subdirectories false
          --fastq-gzip-compression-level 1
          --bcl-num-parallel-tiles "$parallel_tiles"
          --bcl-num-conversion-threads "$conversion_threads"
          --bcl-num-compression-threads "$compression_threads"
          --bcl-num-decompression-threads "$decompression_threads"
          --shared-thread-odirect-output false
        )
        force_arg=
        if [ -n "$force_arg" ]; then
            bcl_flags+=("$force_arg")
        fi

        printf 'bcl-convert command:' >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        printf ' %q' singularity exec docker://nfcore/bclconvert:4.0.3 bcl-convert "${bcl_flags[@]}" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        printf '\n' >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        singularity exec docker://nfcore/bclconvert:4.0.3 bcl-convert "${bcl_flags[@]}" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log 2>&1

        if [ "$staging_mode" = "dev_shm" ] || [ "$staging_mode" = "mounted_dev_shm" ] || [ "$staging_mode" = "s3_dev_shm" ] || [ "$staging_mode" = "output_dev_shm" ]; then
            echo "Copying BCLConvert outputs from scratch to result tree: $(date -Is)" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
            cp -a "$effective_output_dir"/. results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/
            df -h "$scratch_root" results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log 2>&1 || true
        fi
        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
        echo "run_bclconvert finished: $(date -Is)" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
        touch results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done


[Sat May 30 05:56:10 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: 3
    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/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, 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


[Sat May 30 05:56:10 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: 4
    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/rollup.json, 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/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv; 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/fastqs/Reports/fastq_list.csv, 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/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


[Sat May 30 05:56:10 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: 5
    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/rollup.json, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/demultiplex_stats.tsv, 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
    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


[Sat May 30 05:56:10 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: 6
    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/Demultiplex_Stats.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs/Reports/fastq_list.csv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, 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


[Sat May 30 05:56:10 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: 0
    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/metrics/demultiplex_stats.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert_metrics_mqc.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/unknown_barcodes.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert.done, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/fastq_manifest.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/generated.units.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/metrics/index_hopping.tsv, results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/multiqc_report.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=

touch results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/bclconvert.bootstrap.complete
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
multiqc_bclconvert                           1              1              1
produce_bclconvert_fastqs_and_metrics        1              1              1
run_bclconvert                               1            192            192
total                                        7              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, multiqc_bclconvert, produce_bclconvert_fastqs_and_metrics, run_bclconvert
    missing output files:
        bclconvert_generate_units_tsv, bclconvert_metrics_multiqc_exports, bclconvert_metrics_summary, bclconvert_validate_inputs, multiqc_bclconvert, produce_bclconvert_fastqs_and_metrics, run_bclconvert

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/ccv20260529r22_illumina_bclconvert_dryrun/daylily-omics-analysis$
