Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/7874ce9d5665147924dae50a682c78/.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/99/7874ce9d5665147924dae50a682c78/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_Z0K-N1-BDNA-1_A23KFG7LT4_1/1029_Z0K-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_Z0K-N1-BDNA-1_A23KFG7LT4_1/1029_Z0K-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_Z0K-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_Z0K-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Z0K-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Z0K-N1-BDNA-1_A23KFG7LT4_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: 78142779 total, 43606 skipped (flags/unmapped)
Fragments: 39155444 total (38915999 tlen-paired, 2868 hash-paired, 405 singletons, 7524 discordant, 228648 orphans, 8669 too large [>5000 bp], 12743829 duplicates)
Reads: 72516461 total, 52431 skipped (flags/unmapped)
Fragments: 36332250 total (36096338 tlen-paired, 3952 hash-paired, 389 singletons, 11092 discordant, 220479 orphans, 10199 too large [>5000 bp], 12104796 duplicates)
Reads: 84519776 total, 46154 skipped (flags/unmapped)
Fragments: 42353552 total (42065291 tlen-paired, 3632 hash-paired, 314 singletons, 11843 discordant, 272472 orphans, 19652 too large [>5000 bp], 14186838 duplicates)
Reads: 85226114 total, 76542 skipped (flags/unmapped)
Fragments: 42788897 total (42129979 tlen-paired, 3428 hash-paired, 333 singletons, 125176 discordant, 529981 orphans, 51046 too large [>5000 bp], 14335562 duplicates)