Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8E2-N1-BDNA-1_A23NLN3LT4_1/1136_8E2-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_8E2-N1-BDNA-1_A23NLN3LT4_1/1136_8E2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/9e312374b60a6a97b2633b66b4c116/.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/95/9e312374b60a6a97b2633b66b4c116/.command.run
==> 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: 1136_8E2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_8E2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8E2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8E2-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: 61730647 total, 48765 skipped (flags/unmapped)
Fragments: 30924316 total (30722817 tlen-paired, 2836 hash-paired, 238 singletons, 12109 discordant, 186316 orphans, 9902 too large [>5000 bp], 9206604 duplicates)
Reads: 66342748 total, 42693 skipped (flags/unmapped)
Fragments: 33239062 total (33016121 tlen-paired, 4057 hash-paired, 239 singletons, 10619 discordant, 208026 orphans, 15098 too large [>5000 bp], 9996129 duplicates)
Reads: 67286671 total, 39494 skipped (flags/unmapped)
Fragments: 33711060 total (33510325 tlen-paired, 2275 hash-paired, 309 singletons, 8483 discordant, 189668 orphans, 7517 too large [>5000 bp], 9865708 duplicates)
Reads: 72889369 total, 65189 skipped (flags/unmapped)
Fragments: 36570303 total (36080212 tlen-paired, 2623 hash-paired, 221 singletons, 92708 discordant, 394539 orphans, 39167 too large [>5000 bp], 11036478 duplicates)