Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8DR-N1-BDNA-1_A23NLN3LT4_1/1136_8DR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8DR-N1-BDNA-1_A23NLN3LT4_1/1136_8DR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/9f71b270eda4f1ed051c58e54a8192/.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/4c/9f71b270eda4f1ed051c58e54a8192/.command.run
==> 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: 1136_8DR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 75216642 total, 55251 skipped (flags/unmapped)
Fragments: 37716343 total (37408080 tlen-paired, 3086 hash-paired, 273 singletons, 15018 discordant, 289886 orphans, 9432 too large [>5000 bp], 12272954 duplicates)
Reads: 80116490 total, 44033 skipped (flags/unmapped)
Fragments: 40176799 total (39863904 tlen-paired, 2650 hash-paired, 427 singletons, 10542 discordant, 299276 orphans, 9281 too large [>5000 bp], 12878364 duplicates)
Reads: 89090400 total, 79058 skipped (flags/unmapped)
Fragments: 44785986 total (43922477 tlen-paired, 2724 hash-paired, 326 singletons, 164703 discordant, 695756 orphans, 67726 too large [>5000 bp], 14697513 duplicates)
Reads: 88403237 total, 50209 skipped (flags/unmapped)
Fragments: 44333271 total (43952412 tlen-paired, 3447 hash-paired, 295 singletons, 15998 discordant, 361119 orphans, 23950 too large [>5000 bp], 14557149 duplicates)