DAY-EC activated.
DAY-EC activated.
aid=ccv20260529r22_illumina_bclconvert
repo=/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis
status_json:
{
  "command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true",
  "completed_at": null,
  "exit_code": null,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis",
  "session_name": "ccv20260529r22_illumina_bclconvert",
  "started_at": "2026-05-30T05:58:29Z"
}
bclconvert_profile:
recent_bcl_logs:
/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis/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
/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis/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
/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
run_bclconvert started: 2026-05-30T06:02:50+00:00
host: i192mem-dy-all-2
threads: 192
resources_mem_mb: 180000
TMPDIR: /fsx/scratch
staging_mode: output_dev_shm
scratch_root: /fsx/scratch/dayoa_bclconvert
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  192G  8.6T   3% /fsx
10.0.1.96@tcp:/d4tzvb4v  8.8T  192G  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. 
/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis/logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.out
/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert/daylily-omics-analysis/logs/slurm/run_bclconvert/run_bclconvert.run_bclconvert.2.err
                ;;
        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
        
slurm_queue:
             JOBID            PARTITION    STATE       TIME TIME_LIMI  NODES                 NAME
              2654              i192mem  RUNNING       0:27 3-18:40:00      1 run_bclconvert-run_b
scratch_usage:
65K	/fsx/scratch/dayoa_bclconvert
/fsx/scratch/dayoa_bclconvert/2654.11051
33K	/fsx/scratch/dayoa_bclconvert/2654.11051
analysis_usage:
376M	/fsx/analysis_results/ubuntu/ccv20260529r22_illumina_bclconvert
