Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/8ee56cfe57594a591ba8ae45ecd500/.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/fa/8ee56cfe57594a591ba8ae45ecd500/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DGN-N1-BDNA-1_B23KFG5LT4_1/1029_DGN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DGN-N1-BDNA-1_B23KFG5LT4_1/1029_DGN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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_DGN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_DGN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DGN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DGN-N1-BDNA-1_B23KFG5LT4_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: 82083428 total, 67264 skipped (flags/unmapped)
Fragments: 41160247 total (40806903 tlen-paired, 4131 hash-paired, 404 singletons, 14571 discordant, 334238 orphans, 15156 too large [>5000 bp], 18204779 duplicates)
Reads: 87252171 total, 52329 skipped (flags/unmapped)
Fragments: 43769096 total (43394830 tlen-paired, 2344 hash-paired, 472 singletons, 10154 discordant, 361296 orphans, 11709 too large [>5000 bp], 18839917 duplicates)
Reads: 87425817 total, 56968 skipped (flags/unmapped)
Fragments: 43854861 total (43457560 tlen-paired, 3627 hash-paired, 317 singletons, 12637 discordant, 380720 orphans, 20082 too large [>5000 bp], 19372842 duplicates)
Reads: 96912753 total, 102219 skipped (flags/unmapped)
Fragments: 48745101 total (47682356 tlen-paired, 4200 hash-paired, 342 singletons, 211517 discordant, 846686 orphans, 83680 too large [>5000 bp], 21479229 duplicates)