Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ac2aa75015ab7720c56938e85f972f/.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/e7/ac2aa75015ab7720c56938e85f972f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BOCP-N1-BDNA-1_B23H2GYLT3_1/1029_BOCP-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BOCP-N1-BDNA-1_B23H2GYLT3_1/1029_BOCP-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_BOCP-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOCP-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOCP-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BOCP-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: 87505484 total, 77882 skipped (flags/unmapped)
Fragments: 43949826 total (43441602 tlen-paired, 13748 hash-paired, 7208 singletons, 9764 discordant, 477504 orphans, 6331 too large [>5000 bp], 10058504 duplicates)
Reads: 95837912 total, 67101 skipped (flags/unmapped)
Fragments: 48153129 total (47577142 tlen-paired, 13458 hash-paired, 7665 singletons, 7340 discordant, 547524 orphans, 9871 too large [>5000 bp], 10989566 duplicates)
Reads: 96591473 total, 69817 skipped (flags/unmapped)
Fragments: 48524018 total (47937853 tlen-paired, 15915 hash-paired, 7735 singletons, 9884 discordant, 552631 orphans, 16993 too large [>5000 bp], 11033418 duplicates)
Reads: 99312374 total, 124471 skipped (flags/unmapped)
Fragments: 50172155 total (48384422 tlen-paired, 15929 hash-paired, 8040 singletons, 347525 discordant, 1416239 orphans, 133936 too large [>5000 bp], 11303083 duplicates)