Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/4679a6d07177b0aad8c99419f0c588/.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/71/4679a6d07177b0aad8c99419f0c588/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_8OI-N1-BDNA-1_2375WFLT3_s19/1029_8OI-N1-BDNA-1_2375WFLT3_s19.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_8OI-N1-BDNA-1_2375WFLT3_s19/1029_8OI-N1-BDNA-1_2375WFLT3_s19.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_8OI-N1-BDNA-1_2375WFLT3_s19.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8OI-N1-BDNA-1_2375WFLT3_s19.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_8OI-N1-BDNA-1_2375WFLT3_s19.recalibrated.bam.bai
The index file is older than the data file: 1029_8OI-N1-BDNA-1_2375WFLT3_s19.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: 76785788 total, 60175 skipped (flags/unmapped)
Fragments: 38594990 total (38075032 tlen-paired, 7867 hash-paired, 1162 singletons, 12658 discordant, 498271 orphans, 17533 too large [>5000 bp], 10877575 duplicates)
Reads: 69250919 total, 61468 skipped (flags/unmapped)
Fragments: 34809568 total (34353613 tlen-paired, 3167 hash-paired, 1049 singletons, 12603 discordant, 439136 orphans, 5250 too large [>5000 bp], 9914672 duplicates)
Reads: 75307231 total, 55423 skipped (flags/unmapped)
Fragments: 37857549 total (37365232 tlen-paired, 2450 hash-paired, 1139 singletons, 9235 discordant, 479493 orphans, 8671 too large [>5000 bp], 10628119 duplicates)
Reads: 78231116 total, 108082 skipped (flags/unmapped)
Fragments: 39552323 total (38042862 tlen-paired, 4454 hash-paired, 1200 singletons, 290327 discordant, 1213480 orphans, 116534 too large [>5000 bp], 11073966 duplicates)