Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BMTS-N1-BDNA-1_A23MHW3LT4_1/1029_BMTS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/a9aae8a3e7b5682218283668805a5f/.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/73/a9aae8a3e7b5682218283668805a5f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BMTS-N1-BDNA-1_A23MHW3LT4_1/1029_BMTS-N1-BDNA-1_A23MHW3LT4_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_BMTS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMTS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMTS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BMTS-N1-BDNA-1_A23MHW3LT4_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: 83348571 total, 71661 skipped (flags/unmapped)
Fragments: 41965101 total (41268065 tlen-paired, 3122 hash-paired, 618 singletons, 13050 discordant, 680246 orphans, 13786 too large [>5000 bp], 16608030 duplicates)
Reads: 88138035 total, 61833 skipped (flags/unmapped)
Fragments: 44384638 total (43654461 tlen-paired, 2936 hash-paired, 606 singletons, 8953 discordant, 717682 orphans, 12607 too large [>5000 bp], 17134201 duplicates)
Reads: 96433135 total, 66957 skipped (flags/unmapped)
Fragments: 48561619 total (47752722 tlen-paired, 5632 hash-paired, 488 singletons, 12627 discordant, 790150 orphans, 16789 too large [>5000 bp], 19258756 duplicates)
Reads: 98592013 total, 105915 skipped (flags/unmapped)
Fragments: 50033793 total (47545454 tlen-paired, 2869 hash-paired, 512 singletons, 495250 discordant, 1989708 orphans, 204366 too large [>5000 bp], 19609539 duplicates)