Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_0NX-N1-BDNA-1_2375WFLT3_s04/1029_0NX-N1-BDNA-1_2375WFLT3_s04.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/51a74a3e0c8cf463afbd8e019fc263/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/51a74a3e0c8cf463afbd8e019fc263/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_0NX-N1-BDNA-1_2375WFLT3_s04/1029_0NX-N1-BDNA-1_2375WFLT3_s04.recalibrated.bam.bai
==> 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_0NX-N1-BDNA-1_2375WFLT3_s04.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_2375WFLT3_s04.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_2375WFLT3_s04.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_2375WFLT3_s04.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: 68453279 total, 59470 skipped (flags/unmapped)
Fragments: 34384118 total (33983798 tlen-paired, 3755 hash-paired, 1064 singletons, 11960 discordant, 383541 orphans, 5089 too large [>5000 bp], 9680530 duplicates)
Reads: 74412879 total, 53415 skipped (flags/unmapped)
Fragments: 37379261 total (36951609 tlen-paired, 2976 hash-paired, 1050 singletons, 8286 discordant, 415340 orphans, 8666 too large [>5000 bp], 10368946 duplicates)
Reads: 75580344 total, 57930 skipped (flags/unmapped)
Fragments: 37961803 total (37520486 tlen-paired, 3709 hash-paired, 1064 singletons, 11580 discordant, 424964 orphans, 12418 too large [>5000 bp], 10587171 duplicates)
Reads: 76714531 total, 99311 skipped (flags/unmapped)
Fragments: 38730569 total (37432672 tlen-paired, 2555 hash-paired, 1108 singletons, 248302 discordant, 1045932 orphans, 100561 too large [>5000 bp], 10759883 duplicates)