Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_F19-N1-BDNA-1_A23TNVNLT4_1/1241_F19-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_F19-N1-BDNA-1_A23TNVNLT4_1/1241_F19-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/975b5ccbff7e764387c155bc892fb4/.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/ba/975b5ccbff7e764387c155bc892fb4/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_F19-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_F19-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_F19-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_F19-N1-BDNA-1_A23TNVNLT4_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: 99723590 total, 61479 skipped (flags/unmapped)
Fragments: 50004905 total (49614778 tlen-paired, 3285 hash-paired, 451 singletons, 15329 discordant, 371062 orphans, 11907 too large [>5000 bp], 18622942 duplicates)
Reads: 106671057 total, 50763 skipped (flags/unmapped)
Fragments: 53495975 total (53091153 tlen-paired, 3012 hash-paired, 482 singletons, 10502 discordant, 390826 orphans, 9826 too large [>5000 bp], 19678305 duplicates)
Reads: 116559243 total, 56865 skipped (flags/unmapped)
Fragments: 58454889 total (57995527 tlen-paired, 3681 hash-paired, 456 singletons, 15527 discordant, 439698 orphans, 16377 too large [>5000 bp], 22024333 duplicates)
Reads: 118739447 total, 108337 skipped (flags/unmapped)
Fragments: 59701202 total (58502344 tlen-paired, 3407 hash-paired, 463 singletons, 234393 discordant, 960595 orphans, 94882 too large [>5000 bp], 22422120 duplicates)