Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/6f6f1219f33b284ee5210e8648c480/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_H5S-N1-BDNA-1_2375WFLT3_s77/1029_H5S-N1-BDNA-1_2375WFLT3_s77.recalibrated.bam
  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/e0/6f6f1219f33b284ee5210e8648c480/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_H5S-N1-BDNA-1_2375WFLT3_s77/1029_H5S-N1-BDNA-1_2375WFLT3_s77.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_H5S-N1-BDNA-1_2375WFLT3_s77.recalibrated.bam.baiThe index file is older than the data file: 1029_H5S-N1-BDNA-1_2375WFLT3_s77.recalibrated.bam.bai
The index file is older than the data file: 1029_H5S-N1-BDNA-1_2375WFLT3_s77.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_H5S-N1-BDNA-1_2375WFLT3_s77.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: 83924357 total, 69024 skipped (flags/unmapped)
Fragments: 42180806 total (41642948 tlen-paired, 3784 hash-paired, 1306 singletons, 14979 discordant, 517789 orphans, 6408 too large [>5000 bp], 13193358 duplicates)
Reads: 91520428 total, 68029 skipped (flags/unmapped)
Fragments: 45997460 total (45413986 tlen-paired, 4748 hash-paired, 1372 singletons, 10529 discordant, 566825 orphans, 12838 too large [>5000 bp], 14141660 duplicates)
Reads: 94674853 total, 118779 skipped (flags/unmapped)
Fragments: 47857227 total (46074360 tlen-paired, 2418 hash-paired, 1408 singletons, 343455 discordant, 1435586 orphans, 139307 too large [>5000 bp], 14734696 duplicates)
Reads: 92619046 total, 69545 skipped (flags/unmapped)
Fragments: 46547411 total (45950895 tlen-paired, 3666 hash-paired, 1360 singletons, 14117 discordant, 577373 orphans, 16706 too large [>5000 bp], 14420416 duplicates)