Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_HT5-N1-BDNA-1_2375WFLT3_s81/1029_HT5-N1-BDNA-1_2375WFLT3_s81.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/86c0ca686328ef88d590661b5e3799/.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/6f/86c0ca686328ef88d590661b5e3799/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_HT5-N1-BDNA-1_2375WFLT3_s81/1029_HT5-N1-BDNA-1_2375WFLT3_s81.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: 1029_HT5-N1-BDNA-1_2375WFLT3_s81.recalibrated.bam.baiThe index file is older than the data file: 1029_HT5-N1-BDNA-1_2375WFLT3_s81.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_HT5-N1-BDNA-1_2375WFLT3_s81.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HT5-N1-BDNA-1_2375WFLT3_s81.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: 71072806 total, 63080 skipped (flags/unmapped)
Fragments: 35756997 total (35223495 tlen-paired, 3781 hash-paired, 1246 singletons, 13219 discordant, 515256 orphans, 6117 too large [>5000 bp], 11009578 duplicates)
Reads: 78570172 total, 62141 skipped (flags/unmapped)
Fragments: 39528880 total (38924460 tlen-paired, 3635 hash-paired, 1287 singletons, 13626 discordant, 585872 orphans, 18715 too large [>5000 bp], 12033275 duplicates)
Reads: 76808875 total, 55668 skipped (flags/unmapped)
Fragments: 38647726 total (38075431 tlen-paired, 2570 hash-paired, 1224 singletons, 9338 discordant, 559163 orphans, 9071 too large [>5000 bp], 11738131 duplicates)
Reads: 80248559 total, 108626 skipped (flags/unmapped)
Fragments: 40653688 total (38854848 tlen-paired, 3368 hash-paired, 1352 singletons, 346953 discordant, 1447167 orphans, 140538 too large [>5000 bp], 12283225 duplicates)