Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_N53-N1-BDNA-1_A23NLN3LT4_1/1029_N53-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/81b3c56c65fb7aae188ce2a783c892/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_N53-N1-BDNA-1_A23NLN3LT4_1/1029_N53-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/4f/81b3c56c65fb7aae188ce2a783c892/.command.run
==> 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_N53-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N53-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N53-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N53-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: 78549016 total, 66740 skipped (flags/unmapped)
Fragments: 39392158 total (39047171 tlen-paired, 3531 hash-paired, 391 singletons, 16950 discordant, 324115 orphans, 11233 too large [>5000 bp], 14181797 duplicates)
Reads: 91684634 total, 60877 skipped (flags/unmapped)
Fragments: 45986032 total (45579196 tlen-paired, 2904 hash-paired, 299 singletons, 17181 discordant, 386452 orphans, 19222 too large [>5000 bp], 16686549 duplicates)
Reads: 83120318 total, 57339 skipped (flags/unmapped)
Fragments: 41684577 total (41339140 tlen-paired, 3531 hash-paired, 455 singletons, 12017 discordant, 329434 orphans, 11857 too large [>5000 bp], 14758875 duplicates)
Reads: 92077546 total, 92425 skipped (flags/unmapped)
Fragments: 46300009 total (45347277 tlen-paired, 3078 hash-paired, 358 singletons, 181503 discordant, 767793 orphans, 76627 too large [>5000 bp], 16791829 duplicates)