Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/113f171ee02ddcb4d774530d175ec1/.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/2d/113f171ee02ddcb4d774530d175ec1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQKE-N1-BDNA-1_2375WFLT3_s47/1029_BQKE-N1-BDNA-1_2375WFLT3_s47.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQKE-N1-BDNA-1_2375WFLT3_s47/1029_BQKE-N1-BDNA-1_2375WFLT3_s47.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BQKE-N1-BDNA-1_2375WFLT3_s47.recalibrated.bam.baiThe index file is older than the data file: 1029_BQKE-N1-BDNA-1_2375WFLT3_s47.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1029_BQKE-N1-BDNA-1_2375WFLT3_s47.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQKE-N1-BDNA-1_2375WFLT3_s47.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: 82419596 total, 66456 skipped (flags/unmapped)
Fragments: 41422712 total (40889284 tlen-paired, 3688 hash-paired, 1328 singletons, 12452 discordant, 515960 orphans, 12502 too large [>5000 bp], 12240917 duplicates)
Reads: 82261567 total, 73210 skipped (flags/unmapped)
Fragments: 41342026 total (40811365 tlen-paired, 4627 hash-paired, 1454 singletons, 15919 discordant, 508661 orphans, 7210 too large [>5000 bp], 12310434 duplicates)
Reads: 89396003 total, 67963 skipped (flags/unmapped)
Fragments: 44926775 total (44357639 tlen-paired, 5083 hash-paired, 1465 singletons, 11595 discordant, 550993 orphans, 13474 too large [>5000 bp], 13198671 duplicates)
Reads: 92548731 total, 116588 skipped (flags/unmapped)
Fragments: 46759115 total (45070620 tlen-paired, 2414 hash-paired, 1509 singletons, 332156 discordant, 1352416 orphans, 133919 too large [>5000 bp], 13741161 duplicates)