Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_G4G-N1-BDNA-1_B23KFG5LT4_1/1029_G4G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e91cb358307ab5b92410c651db83fd/.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/fc/e91cb358307ab5b92410c651db83fd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_G4G-N1-BDNA-1_B23KFG5LT4_1/1029_G4G-N1-BDNA-1_B23KFG5LT4_1.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_G4G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G4G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G4G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G4G-N1-BDNA-1_B23KFG5LT4_1.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: 78733257 total, 59032 skipped (flags/unmapped)
Fragments: 39466730 total (39163148 tlen-paired, 2981 hash-paired, 410 singletons, 19408 discordant, 280783 orphans, 10979 too large [>5000 bp], 14445441 duplicates)
Reads: 84393490 total, 51088 skipped (flags/unmapped)
Fragments: 42300901 total (42000777 tlen-paired, 3045 hash-paired, 386 singletons, 13897 discordant, 282796 orphans, 11891 too large [>5000 bp], 15145047 duplicates)
Reads: 83869067 total, 53073 skipped (flags/unmapped)
Fragments: 42040460 total (41718276 tlen-paired, 5879 hash-paired, 302 singletons, 16381 discordant, 299622 orphans, 17499 too large [>5000 bp], 15472194 duplicates)
Reads: 92172561 total, 84305 skipped (flags/unmapped)
Fragments: 46278907 total (45558304 tlen-paired, 3758 hash-paired, 311 singletons, 133953 discordant, 582581 orphans, 56667 too large [>5000 bp], 17083040 duplicates)