Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/1808a900fa17f9a177d7cf71e72faf/.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/cf/1808a900fa17f9a177d7cf71e72faf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_0DT-N1-BDNA-1_2375WFLT3_s03/1029_0DT-N1-BDNA-1_2375WFLT3_s03.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_0DT-N1-BDNA-1_2375WFLT3_s03/1029_0DT-N1-BDNA-1_2375WFLT3_s03.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_0DT-N1-BDNA-1_2375WFLT3_s03.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_0DT-N1-BDNA-1_2375WFLT3_s03.recalibrated.bam.bai
The index file is older than the data file: 1029_0DT-N1-BDNA-1_2375WFLT3_s03.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0DT-N1-BDNA-1_2375WFLT3_s03.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: 74951315 total, 99831 skipped (flags/unmapped)
Fragments: 37815545 total (36621041 tlen-paired, 3406 hash-paired, 1053 singletons, 227422 discordant, 962623 orphans, 92035 too large [>5000 bp], 11106066 duplicates)
Reads: 66846335 total, 58648 skipped (flags/unmapped)
Fragments: 33568170 total (33192243 tlen-paired, 4409 hash-paired, 1096 singletons, 11847 discordant, 358575 orphans, 5509 too large [>5000 bp], 9974328 duplicates)
Reads: 72366857 total, 55073 skipped (flags/unmapped)
Fragments: 36338644 total (35939651 tlen-paired, 5197 hash-paired, 1013 singletons, 8024 discordant, 384759 orphans, 10134 too large [>5000 bp], 10637225 duplicates)
Reads: 73989300 total, 56482 skipped (flags/unmapped)
Fragments: 37154758 total (36738868 tlen-paired, 3336 hash-paired, 1034 singletons, 11930 discordant, 399590 orphans, 11963 too large [>5000 bp], 10941651 duplicates)