Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/29e310be68998e3bd501c93c5784ad/.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/50/29e310be68998e3bd501c93c5784ad/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_YFY-N1-BDNA-1_A23TNVNLT4_1/1241_YFY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_YFY-N1-BDNA-1_A23TNVNLT4_1/1241_YFY-N1-BDNA-1_A23TNVNLT4_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_YFY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_YFY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_YFY-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_YFY-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: 78312739 total, 51345 skipped (flags/unmapped)
Fragments: 39321464 total (38908912 tlen-paired, 2869 hash-paired, 422 singletons, 11587 discordant, 397674 orphans, 8281 too large [>5000 bp], 15329947 duplicates)
Reads: 83744870 total, 46839 skipped (flags/unmapped)
Fragments: 42056285 total (41611690 tlen-paired, 2554 hash-paired, 450 singletons, 8360 discordant, 433231 orphans, 9571 too large [>5000 bp], 16014648 duplicates)
Reads: 91839716 total, 49338 skipped (flags/unmapped)
Fragments: 46118551 total (45623876 tlen-paired, 2604 hash-paired, 391 singletons, 12189 discordant, 479491 orphans, 16579 too large [>5000 bp], 18027330 duplicates)
Reads: 93858783 total, 89008 skipped (flags/unmapped)
Fragments: 47336134 total (45928719 tlen-paired, 2750 hash-paired, 399 singletons, 280906 discordant, 1123360 orphans, 110633 too large [>5000 bp], 18408464 duplicates)