Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/090e0241cedd69da31566778bb4c5d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BH0W-N1-BDNA-1_B23KFG5LT4_1/1029_BH0W-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/b9/090e0241cedd69da31566778bb4c5d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BH0W-N1-BDNA-1_B23KFG5LT4_1/1029_BH0W-N1-BDNA-1_B23KFG5LT4_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: 1029_BH0W-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BH0W-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BH0W-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BH0W-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: 72990410 total, 56849 skipped (flags/unmapped)
Fragments: 36592184 total (36306776 tlen-paired, 2657 hash-paired, 416 singletons, 12598 discordant, 269737 orphans, 9673 too large [>5000 bp], 15528566 duplicates)
Reads: 78999254 total, 46853 skipped (flags/unmapped)
Fragments: 39614438 total (39310306 tlen-paired, 2208 hash-paired, 489 singletons, 9097 discordant, 292338 orphans, 8176 too large [>5000 bp], 16358114 duplicates)
Reads: 79632323 total, 50355 skipped (flags/unmapped)
Fragments: 39928876 total (39592512 tlen-paired, 4366 hash-paired, 332 singletons, 11076 discordant, 320590 orphans, 22569 too large [>5000 bp], 16984379 duplicates)
Reads: 88484775 total, 91202 skipped (flags/unmapped)
Fragments: 44466819 total (43616206 tlen-paired, 3959 hash-paired, 470 singletons, 170133 discordant, 676051 orphans, 68228 too large [>5000 bp], 18918681 duplicates)