Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/c1fa2a00f3d3c73995b95e9a3ee046/.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/36/c1fa2a00f3d3c73995b95e9a3ee046/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BDOZ-N1-BDNA-1_2375WFLT3_s26/1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BDOZ-N1-BDNA-1_2375WFLT3_s26/1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.recalibrated.bam.bai
==> 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_BDOZ-N1-BDNA-1_2375WFLT3_s26.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26.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: 80673482 total, 70495 skipped (flags/unmapped)
Fragments: 40542526 total (40028374 tlen-paired, 3419 hash-paired, 1326 singletons, 15026 discordant, 494381 orphans, 6821 too large [>5000 bp], 12298228 duplicates)
Reads: 81137929 total, 64799 skipped (flags/unmapped)
Fragments: 40777451 total (40241415 tlen-paired, 7417 hash-paired, 1186 singletons, 12473 discordant, 514960 orphans, 17187 too large [>5000 bp], 12232465 duplicates)
Reads: 91004398 total, 118597 skipped (flags/unmapped)
Fragments: 45974083 total (44316443 tlen-paired, 4217 hash-paired, 1388 singletons, 328140 discordant, 1323895 orphans, 131459 too large [>5000 bp], 13762085 duplicates)
Reads: 87586258 total, 62012 skipped (flags/unmapped)
Fragments: 44022176 total (43467464 tlen-paired, 3029 hash-paired, 1340 singletons, 10917 discordant, 539426 orphans, 10330 too large [>5000 bp], 13124240 duplicates)