Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_2R3-N1-BDNA-1_A23NLN3LT4_1/1136_2R3-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/94bb944c40be706ecd18034b617786/.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/3d/94bb944c40be706ecd18034b617786/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_2R3-N1-BDNA-1_A23NLN3LT4_1/1136_2R3-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] The index file is older than the data file: 1136_2R3-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2R3-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2R3-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2R3-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
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: 75585367 total, 52733 skipped (flags/unmapped)
Fragments: 37876756 total (37621549 tlen-paired, 3222 hash-paired, 370 singletons, 15243 discordant, 236372 orphans, 7932 too large [>5000 bp], 12959064 duplicates)
Reads: 81506667 total, 48309 skipped (flags/unmapped)
Fragments: 40845588 total (40554286 tlen-paired, 3244 hash-paired, 286 singletons, 13442 discordant, 274330 orphans, 20899 too large [>5000 bp], 14135821 duplicates)
Reads: 82171297 total, 47092 skipped (flags/unmapped)
Fragments: 41175601 total (40915224 tlen-paired, 3052 hash-paired, 384 singletons, 10972 discordant, 245969 orphans, 9678 too large [>5000 bp], 13878316 duplicates)
Reads: 89958802 total, 74482 skipped (flags/unmapped)
Fragments: 45151560 total (44512126 tlen-paired, 2528 hash-paired, 354 singletons, 121528 discordant, 515024 orphans, 48289 too large [>5000 bp], 15648381 duplicates)