Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_2VZ-N1-BDNA-1_B23L5TMLT4_1/1029_2VZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/76217b68631b2d0cdb7cfd2ad73e22/.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/30/76217b68631b2d0cdb7cfd2ad73e22/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_2VZ-N1-BDNA-1_B23L5TMLT4_1/1029_2VZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> 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_2VZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_2VZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_2VZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_2VZ-N1-BDNA-1_B23L5TMLT4_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: 79694930 total, 65338 skipped (flags/unmapped)
Fragments: 39968126 total (39620154 tlen-paired, 4276 hash-paired, 426 singletons, 12426 discordant, 330844 orphans, 12305 too large [>5000 bp], 14687187 duplicates)
Reads: 85293223 total, 53044 skipped (flags/unmapped)
Fragments: 42782444 total (42426226 tlen-paired, 3271 hash-paired, 463 singletons, 8694 discordant, 343790 orphans, 9772 too large [>5000 bp], 15542599 duplicates)
Reads: 92603248 total, 58328 skipped (flags/unmapped)
Fragments: 46451542 total (46041559 tlen-paired, 3783 hash-paired, 395 singletons, 12598 discordant, 393207 orphans, 17719 too large [>5000 bp], 17187509 duplicates)
Reads: 93697265 total, 99398 skipped (flags/unmapped)
Fragments: 47143329 total (46072754 tlen-paired, 3333 hash-paired, 450 singletons, 207055 discordant, 859737 orphans, 85698 too large [>5000 bp], 17396374 duplicates)