Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/3106aa955294855a7a69736d55b9b0/.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/1a/3106aa955294855a7a69736d55b9b0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-37bc93-N1_B23T7FYLT4_1/aih-tih-sc-37bc93-N1_B23T7FYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-37bc93-N1_B23T7FYLT4_1/aih-tih-sc-37bc93-N1_B23T7FYLT4_1.recalibrated.bam.bai
==> 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: aih-tih-sc-37bc93-N1_B23T7FYLT4_1.recalibrated.bam.baiThe index file is older than the data file: aih-tih-sc-37bc93-N1_B23T7FYLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-37bc93-N1_B23T7FYLT4_1.recalibrated.bam.baiThe index file is older than the data file: aih-tih-sc-37bc93-N1_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: 321828100 total, 239452 skipped (flags/unmapped)
Fragments: 161841125 total (159610527 tlen-paired, 17817 hash-paired, 2175 singletons, 42671 discordant, 2167935 orphans, 38254 too large [>5000 bp], 85476768 duplicates)
Reads: 348956862 total, 216232 skipped (flags/unmapped)
Fragments: 175521646 total (173001666 tlen-paired, 14825 hash-paired, 1766 singletons, 37337 discordant, 2466052 orphans, 82578 too large [>5000 bp], 93974048 duplicates)
Reads: 355027154 total, 201176 skipped (flags/unmapped)
Fragments: 178604846 total (176107204 tlen-paired, 14023 hash-paired, 2311 singletons, 30323 discordant, 2450985 orphans, 34791 too large [>5000 bp], 94188328 duplicates)
Reads: 392903493 total, 434037 skipped (flags/unmapped)
Fragments: 198784801 total (190681340 tlen-paired, 17260 hash-paired, 2303 singletons, 1691661 discordant, 6392237 orphans, 647197 too large [>5000 bp], 105143212 duplicates)