Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_C35-N1-BDNA-1_235YY7LT3_1/1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_C35-N1-BDNA-1_235YY7LT3_1/1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/7cc299a68db0c5e59ae78e1b7babfe/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/7cc299a68db0c5e59ae78e1b7babfe/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 71277804 total, 57903 skipped (flags/unmapped)
Fragments: 35759205 total (35421277 tlen-paired, 7060 hash-paired, 3811 singletons, 9655 discordant, 317402 orphans, 11352 too large [>5000 bp], 8290848 duplicates)
Reads: 70972203 total, 59736 skipped (flags/unmapped)
Fragments: 35608411 total (35277614 tlen-paired, 4618 hash-paired, 3816 singletons, 11700 discordant, 310663 orphans, 5062 too large [>5000 bp], 8334909 duplicates)
Reads: 77699100 total, 54342 skipped (flags/unmapped)
Fragments: 38982018 total (38632460 tlen-paired, 4620 hash-paired, 4174 singletons, 8998 discordant, 331766 orphans, 8331 too large [>5000 bp], 8955201 duplicates)
Reads: 79122101 total, 84333 skipped (flags/unmapped)
Fragments: 39833488 total (38857019 tlen-paired, 4273 hash-paired, 4220 singletons, 187536 discordant, 780440 orphans, 77726 too large [>5000 bp], 9225772 duplicates)