Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/dcaa8f45ca0599fc46ebb70ddbdc17/.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/17/dcaa8f45ca0599fc46ebb70ddbdc17/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_282-N1-BDNA-1_A23MHW3LT4_1/1136_282-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_282-N1-BDNA-1_A23MHW3LT4_1/1136_282-N1-BDNA-1_A23MHW3LT4_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: 1136_282-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_282-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_282-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_282-N1-BDNA-1_A23MHW3LT4_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: 95989185 total, 64580 skipped (flags/unmapped)
Fragments: 48179804 total (47698082 tlen-paired, 3187 hash-paired, 627 singletons, 17420 discordant, 460488 orphans, 13056 too large [>5000 bp], 17473516 duplicates)
Reads: 102189029 total, 53516 skipped (flags/unmapped)
Fragments: 51291824 total (50803724 tlen-paired, 3039 hash-paired, 690 singletons, 11930 discordant, 472441 orphans, 12498 too large [>5000 bp], 18252775 duplicates)
Reads: 111640445 total, 60478 skipped (flags/unmapped)
Fragments: 56040611 total (55486406 tlen-paired, 3983 hash-paired, 512 singletons, 17275 discordant, 532435 orphans, 15846 too large [>5000 bp], 20427404 duplicates)
Reads: 113219886 total, 96438 skipped (flags/unmapped)
Fragments: 57038947 total (55549798 tlen-paired, 1276 hash-paired, 613 singletons, 289921 discordant, 1197339 orphans, 121753 too large [>5000 bp], 20766794 duplicates)