Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BUFE-N1-BDNA-1_A23TNVNLT4_1/1241_BUFE-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/8d9c6b5eb073c5580d29088dcc75f2/.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/80/8d9c6b5eb073c5580d29088dcc75f2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BUFE-N1-BDNA-1_A23TNVNLT4_1/1241_BUFE-N1-BDNA-1_A23TNVNLT4_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: 1241_BUFE-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BUFE-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BUFE-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BUFE-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: 112449466 total, 79325 skipped (flags/unmapped)
Fragments: 56363030 total (55953755 tlen-paired, 4867 hash-paired, 633 singletons, 20707 discordant, 383068 orphans, 13891 too large [>5000 bp], 21413861 duplicates)
Reads: 121051309 total, 65599 skipped (flags/unmapped)
Fragments: 60678956 total (60264238 tlen-paired, 4121 hash-paired, 657 singletons, 13655 discordant, 396285 orphans, 12370 too large [>5000 bp], 22708064 duplicates)
Reads: 131813061 total, 72617 skipped (flags/unmapped)
Fragments: 66076481 total (65613025 tlen-paired, 5229 hash-paired, 466 singletons, 20111 discordant, 437650 orphans, 12799 too large [>5000 bp], 25299545 duplicates)
Reads: 133697880 total, 128923 skipped (flags/unmapped)
Fragments: 67156981 total (66011140 tlen-paired, 5650 hash-paired, 530 singletons, 218858 discordant, 920803 orphans, 88164 too large [>5000 bp], 25679858 duplicates)