Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/dce25c0748f27a7200a039a021a544/.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/1e/dce25c0748f27a7200a039a021a544/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BXXW-N1-BDNA-1_A23TY32LT4_1/1241_BXXW-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BXXW-N1-BDNA-1_A23TY32LT4_1/1241_BXXW-N1-BDNA-1_A23TY32LT4_1.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: 1241_BXXW-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXXW-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXXW-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXXW-N1-BDNA-1_A23TY32LT4_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: 78640879 total, 48254 skipped (flags/unmapped)
Fragments: 39515013 total (39033366 tlen-paired, 5365 hash-paired, 277 singletons, 10163 discordant, 465842 orphans, 14359 too large [>5000 bp], 16413286 duplicates)
Reads: 71443810 total, 44975 skipped (flags/unmapped)
Fragments: 35901138 total (35471731 tlen-paired, 2608 hash-paired, 351 singletons, 6814 discordant, 419634 orphans, 8272 too large [>5000 bp], 14630161 duplicates)
Reads: 66178556 total, 52901 skipped (flags/unmapped)
Fragments: 33247032 total (32848019 tlen-paired, 3226 hash-paired, 354 singletons, 10112 discordant, 385321 orphans, 8633 too large [>5000 bp], 13768820 duplicates)
Reads: 80034414 total, 85214 skipped (flags/unmapped)
Fragments: 40420228 total (39029205 tlen-paired, 3523 hash-paired, 320 singletons, 278008 discordant, 1109172 orphans, 109118 too large [>5000 bp], 16636922 duplicates)