Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/4272864e3822eb12a88b1e3097e016/.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/42/4272864e3822eb12a88b1e3097e016/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_YYT-N1-BDNA-1_B23H3Y2LT3_1/869_YYT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_YYT-N1-BDNA-1_B23H3Y2LT3_1/869_YYT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
==> 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: 869_YYT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_YYT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_YYT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_YYT-N1-BDNA-1_B23H3Y2LT3_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: 78344850 total, 68033 skipped (flags/unmapped)
Fragments: 39445334 total (38787466 tlen-paired, 6907 hash-paired, 2560 singletons, 7600 discordant, 640801 orphans, 14755 too large [>5000 bp], 8157806 duplicates)
Reads: 78154646 total, 78522 skipped (flags/unmapped)
Fragments: 39335263 total (38707992 tlen-paired, 8002 hash-paired, 2516 singletons, 8771 discordant, 607982 orphans, 8048 too large [>5000 bp], 8185415 duplicates)
Reads: 86364212 total, 69845 skipped (flags/unmapped)
Fragments: 43483807 total (42771618 tlen-paired, 7792 hash-paired, 2914 singletons, 6518 discordant, 694965 orphans, 12316 too large [>5000 bp], 8987184 duplicates)
Reads: 88782660 total, 164575 skipped (flags/unmapped)
Fragments: 45034158 total (42767079 tlen-paired, 8553 hash-paired, 3085 singletons, 452855 discordant, 1802586 orphans, 177720 too large [>5000 bp], 9154343 duplicates)