DAY-EC activated.
DAY-EC activated.
=== now ===
2026-05-30T13:02:53Z
=== status ===
{
  "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/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis",
  "session_name": "ccv20260529r39_illumina_bclconvert",
  "started_at": "2026-05-30T10:10:02Z"
}
=== squeue ===
JOBID|PARTITION|CPUS|ST|TIME|NODES|NODELIST(REASON)|NAME
3310|i192mem|192|R|2:52:25|1|i192mem-dy-all-1|run_bclconvert-run_bclconvert
=== repo config bclconvert ===
111:bclconvert:
112:    run_dir: ""
113:    sample_sheet: "SampleSheet.csv"
114:    output_root: "results/bclconvert"
115:    run_id: ""
116:    libprep: "PCR-FREE"
117:    seq_vendor: "ILMN"
118:    seq_platform_override: ""
119:    force: "true"
120:    keep_undetermined_fastqs: true
121:    sampleproject_subdirectories: false
122:    strict_mode: false
123:    first_tile_only: false
124:    extra_args: ""
125:    threads: 192
126:    mem_mb: 180000
127:    partition: "i192mem"
128:    tmpdir: "/fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch"
129:    staging_mode: "mounted_dev_shm"
130:    scratch_root: "/fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch"
131:    scratch_size_multiplier: "1"
132:    retain_scratch: false
133:    mounted_stage_jobs: 64
134:    parallel_tiles: 8
135:    conversion_threads: 8
136:    compression_threads: 12
137:    decompression_threads: 4
138:    fastq_gzip_compression_level: 1
139:    shared_thread_odirect_output: false
140:
=== run log exists ===
-rw-rw-r-- 1 ubuntu ubuntu 3.0K May 30 10:54 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
=== bcl command/progress markers ===
1:run_bclconvert started: 2026-05-30T10:10:34+00:00
6:staging_mode: mounted_dev_shm
7:scratch_root: /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch
16:INFO:    Using cached SIF image
19:scratch_dir: /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321
20:scratch_input_basis: mounted_metadata_plus_lane_root
21:scratch_root_file_bytes: 4536017
22:scratch_intensities_file_bytes: 52032652
23:scratch_lane_root_disk_bytes: 3415224586752
24:scratch_input_disk_bytes: 3415281155421
25:scratch_input_apparent_bytes: 3415281155421
26:scratch_required_bytes: 3416354897245
27:scratch_available_bytes: 5900225085440
29:mounted_stage_lanes: L001 L002 L003 L004 L005 L006 L007 L008
30:mounted_stage_jobs: 64
31:mounted_stage_cycle_dirs: 2576
32:mounted_stage_regular_files: 11424
40:bcl_num_parallel_tiles: 8
41:bcl_num_conversion_threads: 8
42:bcl_num_compression_threads: 12
43:bcl_num_decompression_threads: 4
44:bcl-convert command: singularity exec docker://nfcore/bclconvert:4.0.3 bcl-convert --bcl-input-directory /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321/run --output-directory /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321/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
45:INFO:    Using cached SIF image
=== run log tail ===
run_bclconvert started: 2026-05-30T10:10:34+00:00
host: i192mem-dy-all-1
threads: 192
resources_mem_mb: 180000
TMPDIR: /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch
staging_mode: mounted_dev_shm
scratch_root: /fsx/analysis_results/ubuntu/ccv20260529r39_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  3.4T  5.4T  39% /fsx
10.0.1.96@tcp:/d4tzvb4v  8.8T  3.4T  5.4T  39% /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/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321
scratch_input_basis: mounted_metadata_plus_lane_root
scratch_root_file_bytes: 4536017
scratch_intensities_file_bytes: 52032652
scratch_lane_root_disk_bytes: 3415224586752
scratch_input_disk_bytes: 3415281155421
scratch_input_apparent_bytes: 3415281155421
scratch_required_bytes: 3416354897245
scratch_available_bytes: 5900225085440
Staging mounted BCL run directory to scratch: 2026-05-30T10:10:38+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: 2026-05-30T10:10:41+00:00
Copying root-level BCL metadata
Skipping InterOp during BCLConvert scratch staging; run-QC rules own InterOp parsing
Mounted scratch staging complete: 2026-05-30T10:54:38+00:00
3.0T	/fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321/run
Filesystem               Size  Used Avail Use% Mounted on
10.0.1.96@tcp:/d4tzvb4v  8.8T  6.5T  2.3T  75% /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/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321/run --output-directory /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/.bclconvert_scratch/3310.25321/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 dirs ===
=== result sizes ===
316K	/fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert
2026-05-30T10:10:28.0000000000 0 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/validated.ok
2026-05-30T10:10:28.0000000000 259 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.log
2026-05-30T10:10:28.0000000000 259 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/bclconvert_validate_inputs.warnings.log
2026-05-30T10:10:28.0000000000 305 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/benchmarks/bclconvert_validate_inputs.bench.tsv
2026-05-30T10:10:28.0000000000 4385 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/tables/samplesheet_rows.tsv
2026-05-30T10:10:28.0000000000 5714 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/normalized.SampleSheet.csv
2026-05-30T10:10:38.0000000000 117 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/mounted_metadata.log
2026-05-30T10:10:41.0000000000 0 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/mounted_files.log
2026-05-30T10:54:45.0000000000 3018 /fsx/analysis_results/ubuntu/ccv20260529r39_illumina_bclconvert/daylily-omics-analysis/results/runs/20260514_LH01106_0009_B23TVLGLT4/bclconvert/logs/run_bclconvert.log
