Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/19597009279b67adf5d9f4b3bf6fe1/.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/e2/19597009279b67adf5d9f4b3bf6fe1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BN7N-N1-BDNA-1_A23NLN3LT4_1/1029_BN7N-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BN7N-N1-BDNA-1_A23NLN3LT4_1/1029_BN7N-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] [W::hts_idx_load3] The index file is older than the data file: 1029_BN7N-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BN7N-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN7N-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN7N-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 75352889 total, 64020 skipped (flags/unmapped)
Fragments: 37802048 total (37440624 tlen-paired, 4372 hash-paired, 397 singletons, 17969 discordant, 338686 orphans, 11928 too large [>5000 bp], 13075326 duplicates)
Reads: 80273018 total, 54158 skipped (flags/unmapped)
Fragments: 40272818 total (39908009 tlen-paired, 3434 hash-paired, 415 singletons, 12391 discordant, 348569 orphans, 11104 too large [>5000 bp], 13695226 duplicates)
Reads: 88475579 total, 59820 skipped (flags/unmapped)
Fragments: 44391489 total (43954245 tlen-paired, 3589 hash-paired, 330 singletons, 18792 discordant, 414533 orphans, 23822 too large [>5000 bp], 15448028 duplicates)
Reads: 89435488 total, 88787 skipped (flags/unmapped)
Fragments: 44998460 total (43996504 tlen-paired, 3723 hash-paired, 367 singletons, 191168 discordant, 806698 orphans, 78423 too large [>5000 bp], 15658250 duplicates)