Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_0YQ-N1-BDNA-1_B23H2GYLT3_1/1136_0YQ-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/1136_0YQ-N1-BDNA-1_B23H2GYLT3_1/1136_0YQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/9fde2a45584705d3704e704dbaa320/.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/51/9fde2a45584705d3704e704dbaa320/.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: 1136_0YQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YQ-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: 110581717 total, 95748 skipped (flags/unmapped)
Fragments: 55535490 total (54904101 tlen-paired, 13762 hash-paired, 9273 singletons, 10958 discordant, 597396 orphans, 10829 too large [>5000 bp], 15314790 duplicates)
Reads: 111265582 total, 85457 skipped (flags/unmapped)
Fragments: 55894758 total (55223988 tlen-paired, 14732 hash-paired, 9269 singletons, 9807 discordant, 636962 orphans, 18420 too large [>5000 bp], 15320453 duplicates)
Reads: 121977612 total, 84851 skipped (flags/unmapped)
Fragments: 61288054 total (60557405 tlen-paired, 14618 hash-paired, 10117 singletons, 8492 discordant, 697422 orphans, 12096 too large [>5000 bp], 16773496 duplicates)
Reads: 125582011 total, 153345 skipped (flags/unmapped)
Fragments: 63425063 total (61204183 tlen-paired, 14815 hash-paired, 10454 singletons, 444223 discordant, 1751388 orphans, 170191 too large [>5000 bp], 17169123 duplicates)