Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/54f4f0be8c0deaa1fa0d60f299bcd4/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/869_EU7-N1-BDNA-1_B23T7FYLT4_1/869_EU7-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
  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/f5/54f4f0be8c0deaa1fa0d60f299bcd4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/869_EU7-N1-BDNA-1_B23T7FYLT4_1/869_EU7-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] [W::hts_idx_load3] The index file is older than the data file: 869_EU7-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.baiThe index file is older than the data file: 869_EU7-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_EU7-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EU7-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: 403800480 total, 300664 skipped (flags/unmapped)
Fragments: 203025800 total (200347312 tlen-paired, 15322 hash-paired, 2802 singletons, 42684 discordant, 2617680 orphans, 34349 too large [>5000 bp], 120992863 duplicates)
Reads: 439703105 total, 272505 skipped (flags/unmapped)
Fragments: 221150294 total (218038263 tlen-paired, 23879 hash-paired, 2602 singletons, 39304 discordant, 3046246 orphans, 89430 too large [>5000 bp], 132246825 duplicates)
Reads: 443627363 total, 263692 skipped (flags/unmapped)
Fragments: 223158846 total (220055138 tlen-paired, 14529 hash-paired, 3165 singletons, 31806 discordant, 3054208 orphans, 51676 too large [>5000 bp], 132076032 duplicates)