Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BK2H-N1-BDNA-1_235YY7LT3_1/1029_BK2H-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/89bf8c2cdb51f37c456f4d405623f5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BK2H-N1-BDNA-1_235YY7LT3_1/1029_BK2H-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  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/a7/89bf8c2cdb51f37c456f4d405623f5/.command.run
==> 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: 1029_BK2H-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BK2H-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_BK2H-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BK2H-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: 66209644 total, 53773 skipped (flags/unmapped)
Fragments: 33225944 total (32903799 tlen-paired, 3797 hash-paired, 4018 singletons, 11055 discordant, 303275 orphans, 5638 too large [>5000 bp], 7670546 duplicates)
Reads: 66005013 total, 52160 skipped (flags/unmapped)
Fragments: 33120509 total (32788879 tlen-paired, 3526 hash-paired, 4012 singletons, 9337 discordant, 314755 orphans, 15301 too large [>5000 bp], 7572060 duplicates)
Reads: 71784873 total, 48527 skipped (flags/unmapped)
Fragments: 36025640 total (35683668 tlen-paired, 3333 hash-paired, 4356 singletons, 8027 discordant, 326256 orphans, 7839 too large [>5000 bp], 8151095 duplicates)
Reads: 73401127 total, 73976 skipped (flags/unmapped)
Fragments: 36975298 total (36009302 tlen-paired, 2082 hash-paired, 4527 singletons, 186145 discordant, 773242 orphans, 77162 too large [>5000 bp], 8437882 duplicates)