Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1136_78D-N1-BDNA-1_B23T7FYLT4_1/1136_78D-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1136_78D-N1-BDNA-1_B23T7FYLT4_1/1136_78D-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/a048b83dfe8de65ea912e0b134d4f3/.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/b5/a048b83dfe8de65ea912e0b134d4f3/.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_78D-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_78D-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_78D-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_78D-N1-BDNA-1_B23T7FYLT4_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: 301824775 total, 225469 skipped (flags/unmapped)
Fragments: 151718067 total (149771563 tlen-paired, 14230 hash-paired, 2253 singletons, 42722 discordant, 1887299 orphans, 26362 too large [>5000 bp], 78762297 duplicates)
Reads: 329489004 total, 201248 skipped (flags/unmapped)
Fragments: 165656850 total (163503018 tlen-paired, 13036 hash-paired, 2572 singletons, 29248 discordant, 2108976 orphans, 42802 too large [>5000 bp], 86214189 duplicates)
Reads: 358649338 total, 214814 skipped (flags/unmapped)
Fragments: 180290083 total (177896975 tlen-paired, 19592 hash-paired, 2073 singletons, 41924 discordant, 2329519 orphans, 92975 too large [>5000 bp], 94829771 duplicates)
Reads: 367344066 total, 428634 skipped (flags/unmapped)
Fragments: 185718837 total (178632601 tlen-paired, 16005 hash-paired, 2637 singletons, 1437975 discordant, 5629619 orphans, 555007 too large [>5000 bp], 96583571 duplicates)