Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/8274dca260eb4b401880709a284651/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_rnafusion/e2e_regression_bcl/rundir/RunParameters.xml
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_rnafusion/e2e_regression_bcl/rundir/SampleSheet.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/8274dca260eb4b401880709a284651/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_rnafusion/e2e_regression_bcl/rundir/RunInfo.xml
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_rnafusion/e2e_regression_bcl/rundir/Data/Intensities/BaseCalls/L003
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_rnafusion/e2e_regression_bcl/rundir/Data/Intensities/L003
==> 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 4 because RunInfo.xml file lists no tiles for it
Sample sheet being processed by common lib? Yes
SampleSheet Settings: 
  OverrideCycles = Y150;I8;I8;Y150

shared-thread-linux-native-asio output is disabled
bcl-convert Version 4.4.6
Copyright (c) 2014-2025 Illumina, Inc.
Command Line: --tiles s_3 --output-directory output --bcl-input-directory rundir --sample-sheet rundir/SampleSheet.csv 
Conversion Begins.
Input BCL Information:
    Read Structure: Y150;I8;I8;Y150
    RunInfo.xml file lists: 4 lanes, 4 tiles
    BCL file format: bcl.gz
    Positions file format: locs
    Filter file format: filter
Conversion Information:
    Tile filtering: converting 1/4 tiles
    Lane 1 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Lane 2 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Lane 4 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count: 2
    Expected number of sample FASTQ files to be created: 4
# CPU hw threads available: 64
Parallel Tiles: 4. Threads Per Tile: 16
SW compressors: 64
SW decompressors: 32
SW FASTQ compression level: 1
Lane 3 Post-run Information:
    Total clusters: 5000000
    Total Genomic Reads: 10000000
    Total Genomic Input Gigabases 1.50
    Minimum reads for a sample: 4999932
    Maximum reads for a sample: 5000068
    Average reads per sample: 5000000.00
    Undetermined reads: 0
Conversion Complete.