Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/1186b2d7c04a55d4f14f47e5ef597f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_469-N1-BDNA-1_A23NLN3LT4_1/1136_469-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/de/1186b2d7c04a55d4f14f47e5ef597f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_469-N1-BDNA-1_A23NLN3LT4_1/1136_469-N1-BDNA-1_A23NLN3LT4_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: 1136_469-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_469-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_469-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_469-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: 71127076 total, 52676 skipped (flags/unmapped)
Fragments: 35676133 total (35362780 tlen-paired, 2629 hash-paired, 368 singletons, 15274 discordant, 295082 orphans, 8792 too large [>5000 bp], 13012254 duplicates)
Reads: 76887186 total, 45280 skipped (flags/unmapped)
Fragments: 38565839 total (38243395 tlen-paired, 2497 hash-paired, 389 singletons, 10793 discordant, 308765 orphans, 9691 too large [>5000 bp], 13703436 duplicates)
Reads: 76095559 total, 48506 skipped (flags/unmapped)
Fragments: 38172413 total (37820782 tlen-paired, 3787 hash-paired, 344 singletons, 13061 discordant, 334439 orphans, 18505 too large [>5000 bp], 13994367 duplicates)
Reads: 84380200 total, 88030 skipped (flags/unmapped)
Fragments: 42426007 total (41549370 tlen-paired, 3292 hash-paired, 364 singletons, 171367 discordant, 701614 orphans, 71067 too large [>5000 bp], 15530403 duplicates)