Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/feb53137fcee7a650a946cf300cf88/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20251009_LH00166_0186_B2372Y3LT4/RunParameters.xml
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20251009_LH00166_0186_B2372Y3LT4/bclconvert_samplesheet_newRNAids.csv
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20251009_LH00166_0186_B2372Y3LT4/Data/Intensities/s.locs
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/feb53137fcee7a650a946cf300cf88/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20251009_LH00166_0186_B2372Y3LT4/RunInfo.xml
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20251009_LH00166_0186_B2372Y3LT4/Data/Intensities/BaseCalls/L004
==> STAGING COMPLETE (7 inputs)

WARNING: skipping lane 1 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 2 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 3 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 5 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 6 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 7 because RunInfo.xml file lists no tiles for it
WARNING: skipping lane 8 because RunInfo.xml file lists no tiles for it
Sample sheet being processed by common lib? Yes
SampleSheet Settings: 
  FastqCompressionFormat = gzip
  NoLaneSplitting = FALSE
  OverrideCycles = Y151;I8;I8;Y151
  SoftwareVersion = 4.3.6

Index Read 2 (i5): The barcode and UMI outputs will be processed and output in Reverse Complement of Sample Sheet inputs. OverrideCycles bases for this read will be interpreted in reverse.
shared-thread-linux-native-asio output is disabled
bcl-convert Version 4.4.6
Copyright (c) 2014-2025 Illumina, Inc.
Command Line: --tiles s_4 --output-directory output --bcl-input-directory rundir --sample-sheet rundir/SampleSheet.csv 
Conversion Begins.
Input BCL Information:
    Read Structure: Y151;I8;I8;Y151
    RunInfo.xml file lists: 8 lanes, 6272 tiles
    BCL file format: cbcl
    Positions file format: slocs
    Filter file format: filter
Conversion Information:
    Tile filtering: converting 784/6272 tiles
    Sample Count for Lane 1: 48
    Lane 1 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 2: 48
    Lane 2 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 3: 48
    Lane 3 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 4: 48
    Sample Count for Lane 5: 24
    Lane 5 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 6: 24
    Lane 6 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 7: 24
    Lane 7 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count for Lane 8: 24
    Lane 8 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Expected number of sample FASTQ files to be created: 96
# CPU hw threads available: 64
Parallel Tiles: 4. Threads Per Tile: 16
SW compressors: 64
SW decompressors: 32
SW FASTQ compression level: 1
Lane 4 Post-run Information:
    Total clusters: 4176716290
    Total Genomic Reads: 8353432580
    Total Genomic Input Gigabases 1261.37
    Minimum reads for a sample: 35210
    Maximum reads for a sample: 419696556
    Average reads per sample: 164842075.92
    Undetermined reads: 441012936
Conversion Complete.