Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BD6O-N1-BDNA-1_A23NLN3LT4_1/1029_BD6O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/021f39082af247852203882a6ccd84/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BD6O-N1-BDNA-1_A23NLN3LT4_1/1029_BD6O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  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/b8/021f39082af247852203882a6ccd84/.command.run
==> 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: 1029_BD6O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BD6O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BD6O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BD6O-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: 60215861 total, 47282 skipped (flags/unmapped)
Fragments: 30160387 total (29973660 tlen-paired, 2961 hash-paired, 197 singletons, 12845 discordant, 170724 orphans, 9363 too large [>5000 bp], 10566002 duplicates)
Reads: 64478632 total, 40207 skipped (flags/unmapped)
Fragments: 32303060 total (32101214 tlen-paired, 2992 hash-paired, 231 singletons, 11095 discordant, 187528 orphans, 10032 too large [>5000 bp], 11350124 duplicates)
Reads: 64934805 total, 37087 skipped (flags/unmapped)
Fragments: 32527323 total (32343574 tlen-paired, 2503 hash-paired, 273 singletons, 8970 discordant, 172003 orphans, 7674 too large [>5000 bp], 11150605 duplicates)
Reads: 70761310 total, 65523 skipped (flags/unmapped)
Fragments: 35482898 total (35067931 tlen-paired, 1912 hash-paired, 256 singletons, 76818 discordant, 335981 orphans, 33114 too large [>5000 bp], 12515616 duplicates)