Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_I1E-N1-BDNA-1_A23TY32LT4_1/1029_I1E-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_I1E-N1-BDNA-1_A23TY32LT4_1/1029_I1E-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/b15a9fb2a1ff112df3ef1ba7de36b6/.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/94/b15a9fb2a1ff112df3ef1ba7de36b6/.command.run
==> 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_I1E-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I1E-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I1E-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I1E-N1-BDNA-1_A23TY32LT4_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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 86132243 total, 62425 skipped (flags/unmapped)
Fragments: 43222840 total (42812168 tlen-paired, 3554 hash-paired, 376 singletons, 13812 discordant, 392930 orphans, 8722 too large [>5000 bp], 17750388 duplicates)
Reads: 93328576 total, 55807 skipped (flags/unmapped)
Fragments: 46839391 total (46395079 tlen-paired, 4635 hash-paired, 343 singletons, 11484 discordant, 427850 orphans, 11090 too large [>5000 bp], 19379506 duplicates)
Reads: 93944709 total, 57141 skipped (flags/unmapped)
Fragments: 47147297 total (46706801 tlen-paired, 3292 hash-paired, 432 singletons, 9990 discordant, 426782 orphans, 10094 too large [>5000 bp], 19005336 duplicates)
Reads: 103560449 total, 98305 skipped (flags/unmapped)
Fragments: 52149317 total (50830893 tlen-paired, 3404 hash-paired, 423 singletons, 264904 discordant, 1049693 orphans, 106813 too large [>5000 bp], 21501015 duplicates)