Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/41f978d5afb4712fdc246fc3c17b2a/.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/ed/41f978d5afb4712fdc246fc3c17b2a/.command.run
==> 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_GNJ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GNJ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GNJ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GNJ-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: 96940796 total, 89564 skipped (flags/unmapped)
Fragments: 48642980 total (48151393 tlen-paired, 21623 hash-paired, 8267 singletons, 11048 discordant, 450649 orphans, 12094 too large [>5000 bp], 11876009 duplicates)
Reads: 105584656 total, 78227 skipped (flags/unmapped)
Fragments: 52999403 total (52453221 tlen-paired, 21239 hash-paired, 8788 singletons, 7632 discordant, 508523 orphans, 12467 too large [>5000 bp], 12916464 duplicates)
Reads: 109490809 total, 135917 skipped (flags/unmapped)
Fragments: 55209692 total (53556678 tlen-paired, 22458 hash-paired, 9216 singletons, 318340 discordant, 1303000 orphans, 123862 too large [>5000 bp], 13271883 duplicates)
Reads: 106589688 total, 78277 skipped (flags/unmapped)
Fragments: 53505191 total (52943848 tlen-paired, 22919 hash-paired, 8841 singletons, 11101 discordant, 518482 orphans, 14176 too large [>5000 bp], 12961401 duplicates)