Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_IZ2-N1-BDNA-1_A23NLN3LT4_1/1029_IZ2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/c222776854198ea140ea7f97fb63bb/.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/f8/c222776854198ea140ea7f97fb63bb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_IZ2-N1-BDNA-1_A23NLN3LT4_1/1029_IZ2-N1-BDNA-1_A23NLN3LT4_1.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_IZ2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IZ2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IZ2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IZ2-N1-BDNA-1_A23NLN3LT4_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: 82228903 total, 57853 skipped (flags/unmapped)
Fragments: 41201223 total (40932922 tlen-paired, 2373 hash-paired, 318 singletons, 13186 discordant, 252424 orphans, 10673 too large [>5000 bp], 14042174 duplicates)
Reads: 88664869 total, 51321 skipped (flags/unmapped)
Fragments: 44431046 total (44134860 tlen-paired, 5243 hash-paired, 291 singletons, 11475 discordant, 279177 orphans, 15462 too large [>5000 bp], 15273212 duplicates)
Reads: 89545338 total, 45934 skipped (flags/unmapped)
Fragments: 44872328 total (44596882 tlen-paired, 1807 hash-paired, 424 singletons, 9111 discordant, 264104 orphans, 9638 too large [>5000 bp], 14974221 duplicates)
Reads: 97808098 total, 83698 skipped (flags/unmapped)
Fragments: 49099221 total (48353777 tlen-paired, 2404 hash-paired, 311 singletons, 146064 discordant, 596665 orphans, 61467 too large [>5000 bp], 16897879 duplicates)