Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/60e67b69ee1bcd12ce7fd7c58ffa7c/.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/20/60e67b69ee1bcd12ce7fd7c58ffa7c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_4J3-N1-BDNA-1_235YY7LT3_1/1029_4J3-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_4J3-N1-BDNA-1_235YY7LT3_1/1029_4J3-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_4J3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_4J3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4J3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4J3-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: 61471516 total, 50923 skipped (flags/unmapped)
Fragments: 30857295 total (30541414 tlen-paired, 2982 hash-paired, 3698 singletons, 10560 discordant, 298641 orphans, 4171 too large [>5000 bp], 7061869 duplicates)
Reads: 66346700 total, 45283 skipped (flags/unmapped)
Fragments: 33304295 total (32973275 tlen-paired, 2817 hash-paired, 3756 singletons, 7276 discordant, 317171 orphans, 6877 too large [>5000 bp], 7487437 duplicates)
Reads: 67437763 total, 50228 skipped (flags/unmapped)
Fragments: 33851292 total (33496692 tlen-paired, 3920 hash-paired, 3919 singletons, 10047 discordant, 336714 orphans, 12792 too large [>5000 bp], 7671872 duplicates)
Reads: 68520570 total, 71940 skipped (flags/unmapped)
Fragments: 34543603 total (33563006 tlen-paired, 2212 hash-paired, 4004 singletons, 186189 discordant, 788192 orphans, 76810 too large [>5000 bp], 7792852 duplicates)