Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/0d8a9d9b437e0ee428456aa593e6a4/.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/bf/0d8a9d9b437e0ee428456aa593e6a4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GGQ-N1-BDNA-1_2375WFLT3_s70/1029_GGQ-N1-BDNA-1_2375WFLT3_s70.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GGQ-N1-BDNA-1_2375WFLT3_s70/1029_GGQ-N1-BDNA-1_2375WFLT3_s70.recalibrated.bam
==> 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_GGQ-N1-BDNA-1_2375WFLT3_s70.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GGQ-N1-BDNA-1_2375WFLT3_s70.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GGQ-N1-BDNA-1_2375WFLT3_s70.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GGQ-N1-BDNA-1_2375WFLT3_s70.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: 59631806 total, 50135 skipped (flags/unmapped)
Fragments: 29977563 total (29581588 tlen-paired, 2864 hash-paired, 891 singletons, 10556 discordant, 381664 orphans, 4550 too large [>5000 bp], 8219933 duplicates)
Reads: 64881501 total, 44728 skipped (flags/unmapped)
Fragments: 32621558 total (32193329 tlen-paired, 2309 hash-paired, 938 singletons, 7325 discordant, 417657 orphans, 6126 too large [>5000 bp], 8800821 duplicates)
Reads: 65771184 total, 49070 skipped (flags/unmapped)
Fragments: 33063375 total (32623151 tlen-paired, 2709 hash-paired, 928 singletons, 10067 discordant, 426520 orphans, 11406 too large [>5000 bp], 8986223 duplicates)
Reads: 67493138 total, 83641 skipped (flags/unmapped)
Fragments: 34136700 total (32806317 tlen-paired, 2102 hash-paired, 977 singletons, 257410 discordant, 1069894 orphans, 103484 too large [>5000 bp], 9210361 duplicates)