Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BN9Y-N1-BDNA-1_2375WFLT3_s39/1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/9b3c02a36a7470a3e5332e1cf77129/.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/83/9b3c02a36a7470a3e5332e1cf77129/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BN9Y-N1-BDNA-1_2375WFLT3_s39/1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.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_BN9Y-N1-BDNA-1_2375WFLT3_s39.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39.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: 50915992 total, 43235 skipped (flags/unmapped)
Fragments: 25592781 total (25242981 tlen-paired, 3179 hash-paired, 853 singletons, 8286 discordant, 337482 orphans, 12765 too large [>5000 bp], 6416468 duplicates)
Reads: 50520223 total, 45582 skipped (flags/unmapped)
Fragments: 25394845 total (25059140 tlen-paired, 2971 hash-paired, 840 singletons, 9407 discordant, 322487 orphans, 4139 too large [>5000 bp], 6426113 duplicates)
Reads: 55612621 total, 42116 skipped (flags/unmapped)
Fragments: 27956103 total (27590693 tlen-paired, 2794 hash-paired, 936 singletons, 6861 discordant, 354819 orphans, 7027 too large [>5000 bp], 6945327 duplicates)
Reads: 56874589 total, 77500 skipped (flags/unmapped)
Fragments: 28748031 total (27664275 tlen-paired, 2745 hash-paired, 985 singletons, 212732 discordant, 867294 orphans, 84653 too large [>5000 bp], 7150085 duplicates)