DAY-EC activated.
DAY-EC activated.
=== analysis ===
/fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis
=== workflow status files ===
2026-05-30T06:33:22.0000000000 2741 ./bin/helpers/fetch_hg38_giabvcf.log
2026-05-30T06:33:22.0000000000 887 ./bin/gen_bcl2fq_ss.py
2026-05-30T06:33:22.0000000000 904 ./bin/helpers/fetch_b37_giabvcf.log
2026-05-30T06:33:23.0000000000 10613 ./docs/plans/bclconvert_plan.md
2026-05-30T06:33:23.0000000000 10995 ./docs/plans/daylily_bclconvert_codex_prompt.md
2026-05-30T06:33:25.0000000000 10637 ./workflow/rules/bcl2fq.smk
2026-05-30T06:33:25.0000000000 11877 ./workflow/scripts/bclconvert_metrics_summary.py
2026-05-30T06:33:25.0000000000 13734 ./workflow/scripts/parse_bclconvert_samplesheet.py
2026-05-30T06:33:25.0000000000 14400 ./tests/test_bclconvert_multiqc.py
2026-05-30T06:33:25.0000000000 22518 ./tests/test_bclconvert_bootstrap.sh
2026-05-30T06:33:25.0000000000 246 ./workflow/envs/bcl2fq_v0.2.yaml
2026-05-30T06:33:25.0000000000 37295 ./workflow/rules/bclconvert.smk
2026-05-30T06:33:25.0000000000 6027 ./workflow/rules/multiqc_for_bcl2fq.smk
2026-05-30T06:33:25.0000000000 7556 ./workflow/scripts/bclconvert_fastq_list_to_units.py
2026-05-30T06:33:25.0000000000 81 ./workflow/envs/bclconvert_metrics_v0.1.yaml
2026-05-30T06:33:25.0000000000 8192 ./workflow/scripts/bclconvert_metrics_to_multiqc.py
2026-05-30T06:33:34.0000000000 397 ./day_cmd.log
2026-05-30T06:33:41.0000000000 33683 ./.snakemake/log/2026-05-30T063336.558591.snakemake.log
2026-05-30T06:33:41.0000000000 3844 ./.snakemake/tmp.zpewo11h/snakejob.run_bclconvert.2.sh
2026-05-30T06:33:41.0000000000 5353 ./sbatch_errs.log
2026-05-30T06:33:44.0000000000 412 ./logs/about.log
=== slurm bcl logs ===
--- logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.err ---
                echo "scratch_input_disk_bytes: $input_disk_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_input_apparent_bytes: $input_apparent_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_required_bytes: $required_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_available_bytes: $available_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                if [ "$available_bytes" -lt "$required_bytes" ]; then
                    echo "Insufficient scratch for bclconvert.staging_mode=s3_dev_shm: required=$required_bytes available=$available_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                run_uri=$(printf "%s" "$source_s3_uri" | sed 's:/*$::')
                lane_root="$effective_run_dir/Data/Intensities/BaseCalls"
                if [ ! -d "$lane_root" ]; then
                    echo "BCL run directory is missing lane root: $lane_root" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                lane_ids=$(find "$lane_root" -mindepth 1 -maxdepth 1 -type d -name 'L[0-9][0-9][0-9]' -printf '%f\n' | sort)
                if [ -z "$lane_ids" ]; then
                    echo "BCL run directory has no L### lane directories under $lane_root" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                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=-f
        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

--- logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.out ---
=== result bcl logs ===
--- logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.err ---
                echo "scratch_input_disk_bytes: $input_disk_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_input_apparent_bytes: $input_apparent_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_required_bytes: $required_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                echo "scratch_available_bytes: $available_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                if [ "$available_bytes" -lt "$required_bytes" ]; then
                    echo "Insufficient scratch for bclconvert.staging_mode=s3_dev_shm: required=$required_bytes available=$available_bytes" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                run_uri=$(printf "%s" "$source_s3_uri" | sed 's:/*$::')
                lane_root="$effective_run_dir/Data/Intensities/BaseCalls"
                if [ ! -d "$lane_root" ]; then
                    echo "BCL run directory is missing lane root: $lane_root" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                fi
                lane_ids=$(find "$lane_root" -mindepth 1 -maxdepth 1 -type d -name 'L[0-9][0-9][0-9]' -printf '%f\n' | sort)
                if [ -z "$lane_ids" ]; then
                    echo "BCL run directory has no L### lane directories under $lane_root" >> results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
                    exit 2
                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=-f
        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

--- logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.out ---
--- results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log ---
WARNING: sample sheet SoftwareVersion 4.3.16 is newer than pinned runtime 4.0.3
INFO: normalized sample sheet SoftwareVersion from 4.3.16 to pinned runtime 4.0.3
INFO: stripped unsupported BCLConvert setting GenerateFastqcMetrics from normalized sample sheet
--- results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.warnings.log ---
WARNING: sample sheet SoftwareVersion 4.3.16 is newer than pinned runtime 4.0.3
INFO: normalized sample sheet SoftwareVersion from 4.3.16 to pinned runtime 4.0.3
INFO: stripped unsupported BCLConvert setting GenerateFastqcMetrics from normalized sample sheet
--- results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log ---
run_bclconvert started: 2026-05-30T06:33:47+00:00
host: i192mem-dy-all-1
threads: 192
resources_mem_mb: 180000
TMPDIR: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch
staging_mode: mounted_dev_shm
scratch_root: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch
bcl_input_directory: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/
source_s3_uri: s3://lsmc-ssf-sequencing-data/basecalls/lsmc/ssf-hq/LH01106/2026/20260514_LH01106_0009_B23TVLGLT4/
output_directory: results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/fastqs
192
Filesystem               Size  Used Avail Use% Mounted on
10.0.1.96@tcp:/d4tzvb4v  8.8T  195G  8.6T   3% /fsx
10.0.1.96@tcp:/d4tzvb4v  8.8T  195G  8.6T   3% /fsx
/usr/bin/singularity
INFO:    Using cached SIF image
bcl-convert Version 00.000.000.4.0.3
Copyright (c) 2014-2018 Illumina, Inc.
scratch_dir: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/2660.35306
scratch_input_basis: mounted_metadata_plus_lane_root
scratch_root_file_bytes: 4536017
scratch_intensities_file_bytes: 52032652
scratch_lane_root_disk_bytes: 92860928
scratch_input_disk_bytes: 149429597
scratch_input_apparent_bytes: 149429597
scratch_required_bytes: 1671460212
scratch_available_bytes: 9361524129792
Staging mounted BCL run directory to scratch: 2026-05-30T06:33:54+00:00
mounted_stage_lanes: L001 L002 L003 L004 L005 L006 L007 L008
mounted_stage_jobs: 64
mounted_stage_cycle_dirs: 2576
mounted_stage_regular_files: 11424
Copying mounted BCL files with sharded cp: 2026-05-30T06:34:06+00:00
Copying root-level BCL metadata
Skipping InterOp during BCLConvert scratch staging; run-QC rules own InterOp parsing
Mounted scratch staging complete: 2026-05-30T08:09:43+00:00
3.0T	/fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/2660.35306/run
Filesystem               Size  Used Avail Use% Mounted on
10.0.1.96@tcp:/d4tzvb4v  8.8T  6.5T  2.3T  74% /fsx
bcl_num_parallel_tiles: 8
bcl_num_conversion_threads: 8
bcl_num_compression_threads: 12
bcl_num_decompression_threads: 4
bcl-convert command: singularity exec docker://nfcore/bclconvert:4.0.3 bcl-convert --bcl-input-directory /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/2660.35306/run --output-directory /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/2660.35306/fastqs --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 8 --bcl-num-conversion-threads 8 --bcl-num-compression-threads 12 --bcl-num-decompression-threads 4 --shared-thread-odirect-output false -f
INFO:    Using cached SIF image
=== scratch summary ===
2026-05-30T09:20:53.0000000000 1033895936 .bclconvert_scratch/2660.35306/fastqs/HG005-c_S15_L002_R2_001.fastq.gz
2026-05-30T09:20:53.0000000000 1043333120 .bclconvert_scratch/2660.35306/fastqs/HG006-c_S18_L002_R1_001.fastq.gz
2026-05-30T09:20:53.0000000000 1051721728 .bclconvert_scratch/2660.35306/fastqs/HG004-c_S12_L002_R1_001.fastq.gz
2--output truncated--