Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/3facb31a583a4c0e50126386e25381/.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/b5/3facb31a583a4c0e50126386e25381/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_7Y1-N1-BDNA-1_235YY7LT3_1/1029_7Y1-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_7Y1-N1-BDNA-1_235YY7LT3_1/1029_7Y1-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_7Y1-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7Y1-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: 51474448 total, 51071 skipped (flags/unmapped)
Fragments: 25999363 total (25406768 tlen-paired, 2670 hash-paired, 3073 singletons, 6498 discordant, 580354 orphans, 4039 too large [>5000 bp], 6851588 duplicates)
Reads: 55161663 total, 51173 skipped (flags/unmapped)
Fragments: 27890650 total (27197326 tlen-paired, 2277 hash-paired, 3201 singletons, 4565 discordant, 683281 orphans, 7836 too large [>5000 bp], 7201352 duplicates)
Reads: 56783873 total, 52440 skipped (flags/unmapped)
Fragments: 28693772 total (27998322 tlen-paired, 3419 hash-paired, 3099 singletons, 6664 discordant, 682268 orphans, 14628 too large [>5000 bp], 7495620 duplicates)
Reads: 59083143 total, 83308 skipped (flags/unmapped)
Fragments: 30249767 total (27958577 tlen-paired, 2645 hash-paired, 3463 singletons, 450550 discordant, 1834532 orphans, 169148 too large [>5000 bp], 7633716 duplicates)