Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1029_BQA8-N1-BDNA-1_B23T7FYLT4_1/1029_BQA8-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/8987fd47a2972de94a565f8c3b82bc/.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/1d/8987fd47a2972de94a565f8c3b82bc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1029_BQA8-N1-BDNA-1_B23T7FYLT4_1/1029_BQA8-N1-BDNA-1_B23T7FYLT4_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: 1029_BQA8-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQA8-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQA8-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQA8-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: 508891023 total, 402441 skipped (flags/unmapped)
Fragments: 255897697 total (252353583 tlen-paired, 24062 hash-paired, 3185 singletons, 70604 discordant, 3446263 orphans, 71318 too large [>5000 bp], 150356871 duplicates)
Reads: 557762323 total, 324442 skipped (flags/unmapped)
Fragments: 280620195 total (276638062 tlen-paired, 16942 hash-paired, 4090 singletons, 48768 discordant, 3912333 orphans, 56957 too large [>5000 bp], 165063010 duplicates)
Reads: 605583416 total, 361994 skipped (flags/unmapped)
Fragments: 304601679 total (300195530 tlen-paired, 23783 hash-paired, 3640 singletons, 72676 discordant, 4306050 orphans, 163877 too large [>5000 bp], 181293735 duplicates)
Reads: 620214053 total, 751953 skipped (flags/unmapped)
Fragments: 313941753 total (300800489 tlen-paired, 32973 hash-paired, 4497 singletons, 2655885 discordant, 10447909 orphans, 1015500 too large [>5000 bp], 184840809 duplicates)