Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_4Z2-N1-BDNA-1_2375WFLT3_s12/1029_4Z2-N1-BDNA-1_2375WFLT3_s12.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/1f0bc4002da575165bc0d9889c51ec/.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/f9/1f0bc4002da575165bc0d9889c51ec/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_4Z2-N1-BDNA-1_2375WFLT3_s12/1029_4Z2-N1-BDNA-1_2375WFLT3_s12.recalibrated.bam
==> 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_4Z2-N1-BDNA-1_2375WFLT3_s12.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4Z2-N1-BDNA-1_2375WFLT3_s12.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4Z2-N1-BDNA-1_2375WFLT3_s12.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4Z2-N1-BDNA-1_2375WFLT3_s12.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: 73770510 total, 61399 skipped (flags/unmapped)
Fragments: 37063175 total (36603530 tlen-paired, 3496 hash-paired, 1059 singletons, 10590 discordant, 444500 orphans, 14160 too large [>5000 bp], 10982933 duplicates)
Reads: 79776279 total, 57719 skipped (flags/unmapped)
Fragments: 40085914 total (39602722 tlen-paired, 2986 hash-paired, 1216 singletons, 8848 discordant, 470142 orphans, 9045 too large [>5000 bp], 11797804 duplicates)
Reads: 73575435 total, 64492 skipped (flags/unmapped)
Fragments: 36966433 total (36517918 tlen-paired, 3790 hash-paired, 1149 singletons, 12266 discordant, 431310 orphans, 5268 too large [>5000 bp], 11064755 duplicates)
Reads: 82426523 total, 107912 skipped (flags/unmapped)
Fragments: 41626103 total (40175363 tlen-paired, 3467 hash-paired, 1268 singletons, 284718 discordant, 1161287 orphans, 114480 too large [>5000 bp], 12281914 duplicates)