Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BDOZ-N1-BDNA-1_235YY7LT3_1/1029_BDOZ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/b3d53138ab306c2a17248775fdaec9/.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/5f/b3d53138ab306c2a17248775fdaec9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BDOZ-N1-BDNA-1_235YY7LT3_1/1029_BDOZ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
==> 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_BDOZ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDOZ-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: 71702571 total, 62195 skipped (flags/unmapped)
Fragments: 35990669 total (35623833 tlen-paired, 2873 hash-paired, 3975 singletons, 11783 discordant, 348205 orphans, 5609 too large [>5000 bp], 9204250 duplicates)
Reads: 80179000 total, 91834 skipped (flags/unmapped)
Fragments: 40407037 total (39275362 tlen-paired, 3630 hash-paired, 4246 singletons, 220677 discordant, 903122 orphans, 90230 too large [>5000 bp], 10200113 duplicates)
Reads: 72051012 total, 58445 skipped (flags/unmapped)
Fragments: 36165308 total (35777960 tlen-paired, 7060 hash-paired, 3921 singletons, 10299 discordant, 366068 orphans, 15970 too large [>5000 bp], 9136049 duplicates)
Reads: 77740242 total, 55657 skipped (flags/unmapped)
Fragments: 39023345 total (38631041 tlen-paired, 2642 hash-paired, 4216 singletons, 8649 discordant, 376797 orphans, 9454 too large [>5000 bp], 9777326 duplicates)