Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_05O-N1-BDNA-1_2375WFLT3_s02/1029_05O-N1-BDNA-1_2375WFLT3_s02.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/37525e71308299cdad5909cfd9b234/.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/53/37525e71308299cdad5909cfd9b234/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_05O-N1-BDNA-1_2375WFLT3_s02/1029_05O-N1-BDNA-1_2375WFLT3_s02.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_05O-N1-BDNA-1_2375WFLT3_s02.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_05O-N1-BDNA-1_2375WFLT3_s02.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_05O-N1-BDNA-1_2375WFLT3_s02.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_05O-N1-BDNA-1_2375WFLT3_s02.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: 85291472 total, 65163 skipped (flags/unmapped)
Fragments: 42849441 total (42341560 tlen-paired, 4517 hash-paired, 1300 singletons, 9353 discordant, 492711 orphans, 10719 too large [>5000 bp], 12574659 duplicates)
Reads: 79103337 total, 68235 skipped (flags/unmapped)
Fragments: 39740610 total (39265932 tlen-paired, 3766 hash-paired, 1248 singletons, 13032 discordant, 456632 orphans, 5881 too large [>5000 bp], 11810238 duplicates)
Reads: 88869316 total, 111188 skipped (flags/unmapped)
Fragments: 44887279 total (43325402 tlen-paired, 4089 hash-paired, 1331 singletons, 299412 discordant, 1257045 orphans, 120973 too large [>5000 bp], 13158640 duplicates)
Reads: 87487626 total, 65301 skipped (flags/unmapped)
Fragments: 43950458 total (43418484 tlen-paired, 3879 hash-paired, 1220 singletons, 12978 discordant, 513897 orphans, 18263 too large [>5000 bp], 12937806 duplicates)