Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/8565cffd3dd65089122899c47d602c/.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/5c/8565cffd3dd65089122899c47d602c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_3N0-N1-BDNA-1_235YY7LT3_1/1029_3N0-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_3N0-N1-BDNA-1_235YY7LT3_1/1029_3N0-N1-BDNA-1_235YY7LT3_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: 1029_3N0-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_3N0-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_3N0-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_3N0-N1-BDNA-1_235YY7LT3_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: 65119789 total, 59283 skipped (flags/unmapped)
Fragments: 32694098 total (32340356 tlen-paired, 3416 hash-paired, 4231 singletons, 10760 discordant, 335335 orphans, 5938 too large [>5000 bp], 8059174 duplicates)
Reads: 65287244 total, 54125 skipped (flags/unmapped)
Fragments: 32779179 total (32408238 tlen-paired, 5041 hash-paired, 4043 singletons, 9807 discordant, 352050 orphans, 15427 too large [>5000 bp], 7978023 duplicates)
Reads: 70398056 total, 50979 skipped (flags/unmapped)
Fragments: 35348207 total (34971904 tlen-paired, 2802 hash-paired, 4330 singletons, 7812 discordant, 361359 orphans, 8176 too large [>5000 bp], 8531365 duplicates)
Reads: 72364392 total, 81969 skipped (flags/unmapped)
Fragments: 36494054 total (35397495 tlen-paired, 3430 hash-paired, 4592 singletons, 211510 discordant, 877027 orphans, 87967 too large [>5000 bp], 8859681 duplicates)