Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_03T-N1-BDNA-1_A23H3NYLT3_1/1136_03T-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_03T-N1-BDNA-1_A23H3NYLT3_1/1136_03T-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/51e0e3c762fc9890ea8e59e3a7f0a8/.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/4b/51e0e3c762fc9890ea8e59e3a7f0a8/.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_03T-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03T-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03T-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03T-N1-BDNA-1_A23H3NYLT3_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: 63610074 total, 57875 skipped (flags/unmapped)
Fragments: 32026429 total (31497638 tlen-paired, 6025 hash-paired, 7024 singletons, 6011 discordant, 509731 orphans, 8048 too large [>5000 bp], 4138785 duplicates)
Reads: 68471075 total, 52498 skipped (flags/unmapped)
Fragments: 34493106 total (33892018 tlen-paired, 9241 hash-paired, 7492 singletons, 5978 discordant, 578377 orphans, 9117 too large [>5000 bp], 4415996 duplicates)
Reads: 70047673 total, 89376 skipped (flags/unmapped)
Fragments: 35630826 total (33648133 tlen-paired, 5275 hash-paired, 7530 singletons, 387215 discordant, 1582673 orphans, 143424 too large [>5000 bp], 4462191 duplicates)
Reads: 69313947 total, 51694 skipped (flags/unmapped)
Fragments: 34926305 total (34307406 tlen-paired, 6253 hash-paired, 7621 singletons, 4919 discordant, 600106 orphans, 8685 too large [>5000 bp], 4454850 duplicates)