Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_GP0-N1-BDNA-1_B23H2GYLT3_1/1029_GP0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/537923eaf0de29863ee342d34d37ef/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_GP0-N1-BDNA-1_B23H2GYLT3_1/1029_GP0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  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/e8/537923eaf0de29863ee342d34d37ef/.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_GP0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GP0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GP0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GP0-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: 89808033 total, 76114 skipped (flags/unmapped)
Fragments: 45059790 total (44626874 tlen-paired, 15395 hash-paired, 6828 singletons, 8032 discordant, 402661 orphans, 10914 too large [>5000 bp], 10260706 duplicates)
Reads: 97999564 total, 63621 skipped (flags/unmapped)
Fragments: 49194252 total (48702011 tlen-paired, 15905 hash-paired, 7421 singletons, 6011 discordant, 462904 orphans, 8882 too large [>5000 bp], 11156690 duplicates)
Reads: 98690842 total, 67154 skipped (flags/unmapped)
Fragments: 49532599 total (49048078 tlen-paired, 16435 hash-paired, 7250 singletons, 7816 discordant, 453020 orphans, 9380 too large [>5000 bp], 11191367 duplicates)
Reads: 101258481 total, 114043 skipped (flags/unmapped)
Fragments: 51061105 total (49545061 tlen-paired, 16928 hash-paired, 7588 singletons, 294558 discordant, 1196970 orphans, 113393 too large [>5000 bp], 11422177 duplicates)