DAY-EC activated.
DAY-EC activated.
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": "2026-05-30T06:10:07Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis",
  "session_name": "ccv20260529r24_illumina_bclconvert",
  "started_at": "2026-05-30T06:08:09Z"
}
tmux_patch_lines:
30:[INFO] Wrote BCL Convert bootstrap samples and units header for 41 samples from /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv
95:	  ... which once run, you will copy the samples.tsv and units.tsv files to config/ in this directory.
109:		cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.tsv
165:[INFO] Patched /fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml bclconvert output scratch to /fsx/scratch for 20260514_LH01106_0009_B23TVLGLT4
168:[1m[40m[38;5;118mExecuting: snakemake --profile=/fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis/config/day_profiles/slurm produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true[0m
172:loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
173:Config file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.
185:A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis/config/units.tsv
192:bclconvert_generate_units_tsv                1              1              1
1665:[5m[48;5;118m[30mRETURN CODE: 1[0m
config_units:
1 /fsx/analysis_results/ubuntu/ccv20260529r24_illumina_bclconvert/daylily-omics-analysis/config/units.tsv
RUNID	SAMPLEID	EXPERIMENTID	LANEID	BARCODEID	LIBPREP	SEQ_VENDOR	SEQ_PLATFORM	ILMN_R1_PATH	ILMN_R2_PATH
active_bcl_config:
109-    partition: "i192,i192mem"
110-
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: false
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/scratch"
129-    staging_mode: "output_dev_shm"
130-    scratch_root: "/fsx/scratch/dayoa_bclconvert"
131-    scratch_size_multiplier: 4
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
run_bclconvert_log:
run_bclconvert started: 2026-05-30T06:09:21+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  194G  8.6T   3% /fsx
10.0.1.96@tcp:/d4tzvb4v  8.8T  194G  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/scratch/dayoa_bclconvert/2657.41370
scratch_input_disk_bytes: 329347072
scratch_input_apparent_bytes: 8442068270195
scratch_required_bytes: 2391130112
scratch_available_bytes: 9363786432512
Filesystem               Size  Used Avail Use% Mounted on
10.0.1.96@tcp:/d4tzvb4v  8.8T  194G  8.6T   3% /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/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/ --output-directory /fsx/scratch/dayoa_bclconvert/2657.41370/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
INFO:    Using cached SIF image
ERROR: Output folder directory structure can not be created at /fsx/scratch/dayoa_bclconvert/2657.41370/fastqs
bcl-convert Version 00.000.000.4.0.3
Copyright (c) 2014-2022 Illumina, Inc.

Run BCL Conversion (BCL directory to *.fastq.gz)
  bcl-convert --bcl-input-directory <BCL_ROOT_DIR> --output-directory <PATH> [options]

Options:
  -h [ --help ]                          Print this help message
  -V [ --version ]                       Print the version and exit
  --output-directory arg                 Output BCL directory for BCL conversion (must be specified)
  -f [ --force ]                         Force: allow destination diretory to already exist
  --bcl-input-directory arg              Input BCL directory for BCL conversion (must be specified)
  --sample-sheet arg                     Path to SampleSheet.csv file (default searched for in --bcl-input-directory)
  --bcl-only-lane arg                    Convert only specified lane number (default all lanes)
  --strict-mode arg                      Abort if any files are missing (false by default)
  --first-tile-only arg                  Only convert first tile of input (for testing & debugging)
  --tiles arg                            Process only a subset of tiles by a regular expression
  --exclude-tiles arg                    Exclude set of tiles by a regular expression
  --bcl-sampleproject-subdirectories arg Output to subdirectories based upon sample sheet 'Sample_Project' column
  --sample-name-column-enabled arg       Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories
  --fastq-gzip-compression-level arg     Set fastq output compression level 0-9 (default 1)
  --shared-thread-odirect-output arg     Use linux native asynchronous io (io_submit) for file output (Default=false)
  --bcl-num-parallel-tiles arg           # of tiles to process in parallel (default 1)
  --bcl-num-conversion-threads arg       # of threads for conversion (per tile, default # cpu threads)
  --bcl-num-compression-threads arg      # of threads for fastq.gz output compression (per tile, default # cpu threads,
                                         or HW+12)
  --bcl-num-decompression-threads arg    # of threads for bcl/cbcl input decompression (per tile, default half # cpu
                                         threads, or HW+8. Only applies when preloading files)
  --bcl-only-matched-reads arg           For pure BCL conversion, do not output files for 'Undetermined' [unmatched]
                                         reads (output by default)
  --run-info arg                         Path to RunInfo.xml file (default root of BCL input directory)
  --no-lane-splitting arg                Do not split FASTQ file by lane (false by default)
  --num-unknown-barcodes-reported arg    # of Top Unknown Barcodes to output (1000 by default)
  --bcl-validate-sample-sheet-only arg   Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
  --output-legacy-stats arg              Also output stats in legacy (bcl2fastq2) format (false by default)
  --no-sample-sheet arg                  Enable legacy no-sample-sheet operation (No demux or trimming. No settings
                                         supported. False by default, not recommended

scratch_tree:
