Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_ROX-N1-BDNA-1_A23H3NYLT3_1/869_ROX-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/376ede54837d376c3878941e1000d2/.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/9d/376ede54837d376c3878941e1000d2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_ROX-N1-BDNA-1_A23H3NYLT3_1/869_ROX-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_ROX-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_ROX-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ROX-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ROX-N1-BDNA-1_A23H3NYLT3_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: 67659043 total, 62111 skipped (flags/unmapped)
Fragments: 33987430 total (33571635 tlen-paired, 14202 hash-paired, 7029 singletons, 6715 discordant, 387849 orphans, 8475 too large [>5000 bp], 3968219 duplicates)
Reads: 73381118 total, 59081 skipped (flags/unmapped)
Fragments: 36882096 total (36399504 tlen-paired, 16026 hash-paired, 7637 singletons, 5925 discordant, 453004 orphans, 9243 too large [>5000 bp], 4266519 duplicates)
Reads: 73162713 total, 59739 skipped (flags/unmapped)
Fragments: 36764560 total (36295258 tlen-paired, 16325 hash-paired, 7603 singletons, 7101 discordant, 438273 orphans, 9865 too large [>5000 bp], 4269595 duplicates)
Reads: 74061632 total, 92295 skipped (flags/unmapped)
Fragments: 37460953 total (35993050 tlen-paired, 14545 hash-paired, 7755 singletons, 284181 discordant, 1161422 orphans, 108304 too large [>5000 bp], 4279267 duplicates)