Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BGMF-N1-BDNA-1_235YY7LT3_1/1029_BGMF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/3e2cb98cc1eccafae7f52fa10e73f0/.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/fb/3e2cb98cc1eccafae7f52fa10e73f0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BGMF-N1-BDNA-1_235YY7LT3_1/1029_BGMF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
==> 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_BGMF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BGMF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGMF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGMF-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: 69596832 total, 55076 skipped (flags/unmapped)
Fragments: 34907567 total (34588520 tlen-paired, 4079 hash-paired, 4073 singletons, 9758 discordant, 301137 orphans, 15916 too large [>5000 bp], 7807764 duplicates)
Reads: 69537111 total, 58111 skipped (flags/unmapped)
Fragments: 34881118 total (34571868 tlen-paired, 4532 hash-paired, 4321 singletons, 10952 discordant, 289445 orphans, 5265 too large [>5000 bp], 7883374 duplicates)
Reads: 75343327 total, 52345 skipped (flags/unmapped)
Fragments: 37792292 total (37468893 tlen-paired, 4267 hash-paired, 4531 singletons, 7948 discordant, 306653 orphans, 8791 too large [>5000 bp], 8400467 duplicates)
Reads: 77380292 total, 81510 skipped (flags/unmapped)
Fragments: 38940647 total (38032381 tlen-paired, 4691 hash-paired, 4760 singletons, 173759 discordant, 725056 orphans, 73652 too large [>5000 bp], 8700900 duplicates)