Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_GCO-N1-BDNA-1_A23NLN3LT4_1/1029_GCO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/a0ddcb7c87e3d4a4327507571ca380/.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/cb/a0ddcb7c87e3d4a4327507571ca380/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_GCO-N1-BDNA-1_A23NLN3LT4_1/1029_GCO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> 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_GCO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GCO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GCO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GCO-N1-BDNA-1_A23NLN3LT4_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: 99412187 total, 70661 skipped (flags/unmapped)
Fragments: 49821916 total (49471615 tlen-paired, 5767 hash-paired, 489 singletons, 17586 discordant, 326459 orphans, 12321 too large [>5000 bp], 17735266 duplicates)
Reads: 107697399 total, 57002 skipped (flags/unmapped)
Fragments: 53979830 total (53622175 tlen-paired, 4044 hash-paired, 553 singletons, 12522 discordant, 340536 orphans, 10913 too large [>5000 bp], 18874919 duplicates)
Reads: 107196645 total, 61249 skipped (flags/unmapped)
Fragments: 53728535 total (53337285 tlen-paired, 4863 hash-paired, 365 singletons, 14963 discordant, 371059 orphans, 24875 too large [>5000 bp], 19286209 duplicates)
Reads: 118171055 total, 103969 skipped (flags/unmapped)
Fragments: 59340328 total (58389547 tlen-paired, 3228 hash-paired, 437 singletons, 184999 discordant, 762117 orphans, 74492 too large [>5000 bp], 21301229 duplicates)