Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3EG-N1-BDNA-1_A23KFG7LT4_1/1136_3EG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/ff2f447becfaf0427eb24aa55484bc/.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/4e/ff2f447becfaf0427eb24aa55484bc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3EG-N1-BDNA-1_A23KFG7LT4_1/1136_3EG-N1-BDNA-1_A23KFG7LT4_1.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: 1136_3EG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3EG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3EG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3EG-N1-BDNA-1_A23KFG7LT4_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: 98152854 total, 68279 skipped (flags/unmapped)
Fragments: 49172592 total (48862755 tlen-paired, 4631 hash-paired, 445 singletons, 17743 discordant, 287018 orphans, 13427 too large [>5000 bp], 17732509 duplicates)
Reads: 104233775 total, 58063 skipped (flags/unmapped)
Fragments: 52220585 total (51911729 tlen-paired, 4175 hash-paired, 567 singletons, 12367 discordant, 291747 orphans, 13428 too large [>5000 bp], 18460781 duplicates)
Reads: 114608874 total, 98687 skipped (flags/unmapped)
Fragments: 57512409 total (56731571 tlen-paired, 3751 hash-paired, 444 singletons, 144570 discordant, 632073 orphans, 58943 too large [>5000 bp], 20898781 duplicates)
Reads: 113892672 total, 60059 skipped (flags/unmapped)
Fragments: 57063463 total (56708950 tlen-paired, 5076 hash-paired, 422 singletons, 18252 discordant, 330763 orphans, 18436 too large [>5000 bp], 20684448 duplicates)