Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BCTO-N1-BDNA-1_235YY7LT3_1/1029_BCTO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/81984806fd0196a0d33a14c385964c/.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/ff/81984806fd0196a0d33a14c385964c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BCTO-N1-BDNA-1_235YY7LT3_1/1029_BCTO-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_BCTO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCTO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCTO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCTO-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: 54914439 total, 48577 skipped (flags/unmapped)
Fragments: 27561626 total (27284552 tlen-paired, 2708 hash-paired, 3499 singletons, 9094 discordant, 261773 orphans, 3941 too large [>5000 bp], 6576838 duplicates)
Reads: 58910496 total, 43522 skipped (flags/unmapped)
Fragments: 29566743 total (29277698 tlen-paired, 2382 hash-paired, 3621 singletons, 6467 discordant, 276575 orphans, 6842 too large [>5000 bp], 6924532 duplicates)
Reads: 61127398 total, 69133 skipped (flags/unmapped)
Fragments: 30807863 total (29955607 tlen-paired, 2418 hash-paired, 3770 singletons, 160931 discordant, 685137 orphans, 65723 too large [>5000 bp], 7240892 duplicates)
Reads: 60372684 total, 47067 skipped (flags/unmapped)
Fragments: 30299090 total (29990500 tlen-paired, 2477 hash-paired, 3695 singletons, 9092 discordant, 293326 orphans, 12229 too large [>5000 bp], 7146062 duplicates)