Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_0NX-N1-BDNA-1_235YY7LT3_1/1029_0NX-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d26905cffd186a8d9cfa104705845c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_0NX-N1-BDNA-1_235YY7LT3_1/1029_0NX-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/86/d26905cffd186a8d9cfa104705845c/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0NX-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: 61689003 total, 51829 skipped (flags/unmapped)
Fragments: 30974928 total (30640169 tlen-paired, 3192 hash-paired, 3381 singletons, 9619 discordant, 318567 orphans, 4633 too large [>5000 bp], 7062184 duplicates)
Reads: 68814480 total, 72801 skipped (flags/unmapped)
Fragments: 34721659 total (33643197 tlen-paired, 2138 hash-paired, 3898 singletons, 204257 discordant, 868169 orphans, 85214 too large [>5000 bp], 7803516 duplicates)
Reads: 67970500 total, 51432 skipped (flags/unmapped)
Fragments: 34127974 total (33756714 tlen-paired, 3161 hash-paired, 3846 singletons, 9245 discordant, 355008 orphans, 10987 too large [>5000 bp], 7701940 duplicates)
Reads: 66662765 total, 47012 skipped (flags/unmapped)
Fragments: 33472773 total (33117500 tlen-paired, 2568 hash-paired, 3636 singletons, 6744 discordant, 342325 orphans, 8084 too large [>5000 bp], 7488570 duplicates)