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/d4/98772d06da47db574f38d8b3a04d30/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/98772d06da47db574f38d8b3a04d30/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_293-N1-BDNA-1_A23NLN3LT4_1/1136_293-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/1136_293-N1-BDNA-1_A23NLN3LT4_1/1136_293-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_293-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_293-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_293-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_293-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: 56462663 total, 45881 skipped (flags/unmapped)
Fragments: 28316016 total (28072254 tlen-paired, 2465 hash-paired, 284 singletons, 9013 discordant, 232000 orphans, 8517 too large [>5000 bp], 9113007 duplicates)
Reads: 60852752 total, 37233 skipped (flags/unmapped)
Fragments: 30523454 total (30267941 tlen-paired, 1711 hash-paired, 361 singletons, 6315 discordant, 247126 orphans, 8049 too large [>5000 bp], 9649182 duplicates)
Reads: 67334808 total, 66126 skipped (flags/unmapped)
Fragments: 33879351 total (33114018 tlen-paired, 2696 hash-paired, 288 singletons, 149841 discordant, 612508 orphans, 61388 too large [>5000 bp], 10932282 duplicates)
Reads: 66849938 total, 41789 skipped (flags/unmapped)
Fragments: 33531584 total (33227380 tlen-paired, 5209 hash-paired, 216 singletons, 9250 discordant, 289529 orphans, 17363 too large [>5000 bp], 10852891 duplicates)