Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6AL-N1-BDNA-1_A23NLN3LT4_1/1136_6AL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/4e4a0a3731326cb86df0df5a2e20af/.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/97/4e4a0a3731326cb86df0df5a2e20af/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_6AL-N1-BDNA-1_A23NLN3LT4_1/1136_6AL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6AL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6AL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6AL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6AL-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: 81446572 total, 61943 skipped (flags/unmapped)
Fragments: 40828687 total (40516006 tlen-paired, 3621 hash-paired, 421 singletons, 16745 discordant, 291894 orphans, 9785 too large [>5000 bp], 14625553 duplicates)
Reads: 88317088 total, 57676 skipped (flags/unmapped)
Fragments: 44265338 total (43952095 tlen-paired, 3906 hash-paired, 483 singletons, 11345 discordant, 297509 orphans, 13364 too large [>5000 bp], 15535690 duplicates)
Reads: 96388281 total, 61953 skipped (flags/unmapped)
Fragments: 48317104 total (47946233 tlen-paired, 5084 hash-paired, 308 singletons, 16937 discordant, 348542 orphans, 20485 too large [>5000 bp], 17421594 duplicates)
Reads: 96815844 total, 93787 skipped (flags/unmapped)
Fragments: 48632340 total (47803658 tlen-paired, 3266 hash-paired, 409 singletons, 155761 discordant, 669246 orphans, 63516 too large [>5000 bp], 17539843 duplicates)