Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/dde61e2f66948b7283e1c8e4bed95e/.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/df/dde61e2f66948b7283e1c8e4bed95e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_FBB-N1-BDNA-1_2375WFLT3_s63/1029_FBB-N1-BDNA-1_2375WFLT3_s63.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_FBB-N1-BDNA-1_2375WFLT3_s63/1029_FBB-N1-BDNA-1_2375WFLT3_s63.recalibrated.bam.bai
==> 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_FBB-N1-BDNA-1_2375WFLT3_s63.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_FBB-N1-BDNA-1_2375WFLT3_s63.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FBB-N1-BDNA-1_2375WFLT3_s63.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FBB-N1-BDNA-1_2375WFLT3_s63.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: 58800224 total, 49043 skipped (flags/unmapped)
Fragments: 29563352 total (29151813 tlen-paired, 4189 hash-paired, 821 singletons, 9157 discordant, 397372 orphans, 11335 too large [>5000 bp], 7895919 duplicates)
Reads: 58370900 total, 52166 skipped (flags/unmapped)
Fragments: 29346860 total (28947405 tlen-paired, 3525 hash-paired, 920 singletons, 11072 discordant, 383938 orphans, 4936 too large [>5000 bp], 7901867 duplicates)
Reads: 64280060 total, 47181 skipped (flags/unmapped)
Fragments: 32322738 total (31883612 tlen-paired, 3232 hash-paired, 1001 singletons, 8221 discordant, 426672 orphans, 7538 too large [>5000 bp], 8555932 duplicates)
Reads: 65785949 total, 89781 skipped (flags/unmapped)
Fragments: 33269018 total (31963165 tlen-paired, 2697 hash-paired, 1020 singletons, 257038 discordant, 1045098 orphans, 102125 too large [>5000 bp], 8829595 duplicates)