Downloading: s3://natera-platform-sandbox/projects/lcvs/flowcells/samplesheets/20260603_LH00166_0309_A23WCJNLT4.samplesheet.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/8ef3ef592f67e68d4732d2ca831221/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/8ef3ef592f67e68d4732d2ca831221/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/illumina_run_folders/data/20260603_LH00166_0309_A23WCJNLT4
==> STAGING COMPLETE (4 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
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
  OverrideCycles = Y150N1;I8;I8;Y150N1

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_3 --output-directory output --bcl-input-directory 20260603_LH00166_0309_A23WCJNLT4 --sample-sheet 20260603_LH00166_0309_A23WCJNLT4.samplesheet.csv 
Conversion Begins.
Input BCL Information:
    Read Structure: Y150;I8;I8;Y150
    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
    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?)
    Lane 5 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Lane 6 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Lane 7 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Lane 8 will be skipped because there are no tiles to convert (not listed in RunInfo.xml tile list?)
    Sample Count: 32
    Expected number of sample FASTQ files to be created: 64
# 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: 4247663132
    Total Genomic Reads: 8495326264
    Total Genomic Input Gigabases 1274.30
    Minimum reads for a sample: 122287940
    Maximum reads for a sample: 366958676
    Average reads per sample: 254349347.50
    Undetermined reads: 356147144
Conversion Complete.