Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_UKQ-N1-BDNA-1_B23H2GYLT3_1/1029_UKQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/e95e27f61f70db17d2034b1fe02f34/.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/47/e95e27f61f70db17d2034b1fe02f34/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_UKQ-N1-BDNA-1_B23H2GYLT3_1/1029_UKQ-N1-BDNA-1_B23H2GYLT3_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_UKQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_UKQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_UKQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_UKQ-N1-BDNA-1_B23H2GYLT3_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: 82654070 total, 71021 skipped (flags/unmapped)
Fragments: 41472506 total (41071584 tlen-paired, 13333 hash-paired, 6734 singletons, 8294 discordant, 372561 orphans, 8666 too large [>5000 bp], 8754316 duplicates)
Reads: 89473561 total, 61625 skipped (flags/unmapped)
Fragments: 44910765 total (44461342 tlen-paired, 14767 hash-paired, 7101 singletons, 5928 discordant, 421627 orphans, 9567 too large [>5000 bp], 9493425 duplicates)
Reads: 90827353 total, 63699 skipped (flags/unmapped)
Fragments: 45584316 total (45127855 tlen-paired, 14537 hash-paired, 7319 singletons, 8356 discordant, 426249 orphans, 14295 too large [>5000 bp], 9570959 duplicates)
Reads: 92887024 total, 108723 skipped (flags/unmapped)
Fragments: 46832054 total (45465263 tlen-paired, 13974 hash-paired, 7391 singletons, 263490 discordant, 1081936 orphans, 101760 too large [>5000 bp], 9744055 duplicates)