Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BLTU-N1-BDNA-1_B23KFG5LT4_1/1029_BLTU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/4d94fab5bb5eef80e30ab357d77a48/.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/fd/4d94fab5bb5eef80e30ab357d77a48/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BLTU-N1-BDNA-1_B23KFG5LT4_1/1029_BLTU-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_BLTU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BLTU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLTU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLTU-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: 66522104 total, 71732 skipped (flags/unmapped)
Fragments: 33631303 total (32781675 tlen-paired, 3737 hash-paired, 476 singletons, 9157 discordant, 836258 orphans, 12250 too large [>5000 bp], 17018972 duplicates)
Reads: 69574755 total, 63707 skipped (flags/unmapped)
Fragments: 35205189 total (34271219 tlen-paired, 4724 hash-paired, 514 singletons, 6290 discordant, 922442 orphans, 11813 too large [>5000 bp], 17301692 duplicates)
Reads: 78137560 total, 68574 skipped (flags/unmapped)
Fragments: 39525280 total (38470932 tlen-paired, 7606 hash-paired, 371 singletons, 9200 discordant, 1037171 orphans, 27984 too large [>5000 bp], 19921253 duplicates)
Reads: 81921039 total, 108549 skipped (flags/unmapped)
Fragments: 41947518 total (38652077 tlen-paired, 5000 hash-paired, 582 singletons, 668843 discordant, 2621016 orphans, 269526 too large [>5000 bp], 20491054 duplicates)