Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BBUO-N1-BDNA-1_A23KFG7LT4_1/1029_BBUO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/204302f0650182c83a82069210b875/.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/58/204302f0650182c83a82069210b875/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BBUO-N1-BDNA-1_A23KFG7LT4_1/1029_BBUO-N1-BDNA-1_A23KFG7LT4_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_BBUO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBUO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBUO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBUO-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: 62940406 total, 47919 skipped (flags/unmapped)
Fragments: 31624560 total (31239045 tlen-paired, 2431 hash-paired, 351 singletons, 9739 discordant, 372994 orphans, 8356 too large [>5000 bp], 11136130 duplicates)
Reads: 67374160 total, 39331 skipped (flags/unmapped)
Fragments: 33859745 total (33451430 tlen-paired, 2013 hash-paired, 462 singletons, 6671 discordant, 399169 orphans, 7485 too large [>5000 bp], 11606023 duplicates)
Reads: 73751058 total, 44506 skipped (flags/unmapped)
Fragments: 37064185 total (36591923 tlen-paired, 2794 hash-paired, 315 singletons, 10162 discordant, 458991 orphans, 18744 too large [>5000 bp], 13059052 duplicates)
Reads: 75162530 total, 71445 skipped (flags/unmapped)
Fragments: 37969618 total (36644197 tlen-paired, 2950 hash-paired, 410 singletons, 263582 discordant, 1058479 orphans, 105369 too large [>5000 bp], 13299546 duplicates)