Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/8954247b2713e5bd2dd412eb5919a9/.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/1f/8954247b2713e5bd2dd412eb5919a9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_USM-N1-BDNA-1_A23TY32LT4_1/1241_USM-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_USM-N1-BDNA-1_A23TY32LT4_1/1241_USM-N1-BDNA-1_A23TY32LT4_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: 1241_USM-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_USM-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_USM-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_USM-N1-BDNA-1_A23TY32LT4_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: 109061830 total, 67893 skipped (flags/unmapped)
Fragments: 54684103 total (54234367 tlen-paired, 4494 hash-paired, 352 singletons, 15611 discordant, 429279 orphans, 27681 too large [>5000 bp], 22430850 duplicates)
Reads: 101517047 total, 78425 skipped (flags/unmapped)
Fragments: 50891770 total (50500630 tlen-paired, 5175 hash-paired, 474 singletons, 17279 discordant, 368212 orphans, 11884 too large [>5000 bp], 20796321 duplicates)
Reads: 110155693 total, 67704 skipped (flags/unmapped)
Fragments: 55226354 total (54818541 tlen-paired, 4442 hash-paired, 451 singletons, 12346 discordant, 390574 orphans, 13153 too large [>5000 bp], 22158361 duplicates)
Reads: 120767308 total, 125883 skipped (flags/unmapped)
Fragments: 60683323 total (59543230 tlen-paired, 4810 hash-paired, 452 singletons, 225014 discordant, 909817 orphans, 92524 too large [>5000 bp], 24896287 duplicates)