Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_MJG-N1-BDNA-1_A23TY32LT4_1/1241_MJG-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/220389131b198f5be456c10b62bcd1/.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/36/220389131b198f5be456c10b62bcd1/.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_MJG-N1-BDNA-1_A23TY32LT4_1/1241_MJG-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] [W::hts_idx_load3] The index file is older than the data file: 1241_MJG-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_MJG-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_MJG-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_MJG-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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: 76794353 total, 44803 skipped (flags/unmapped)
Fragments: 38555781 total (38165261 tlen-paired, 2361 hash-paired, 453 singletons, 7703 discordant, 380003 orphans, 9222 too large [>5000 bp], 15356382 duplicates)
Reads: 71677832 total, 54321 skipped (flags/unmapped)
Fragments: 35981360 total (35608378 tlen-paired, 2701 hash-paired, 409 singletons, 11664 discordant, 358208 orphans, 9704 too large [>5000 bp], 14520264 duplicates)
Reads: 85070605 total, 49669 skipped (flags/unmapped)
Fragments: 42712488 total (42256448 tlen-paired, 4706 hash-paired, 326 singletons, 11918 discordant, 439090 orphans, 17688 too large [>5000 bp], 17329749 duplicates)
Reads: 86433696 total, 87900 skipped (flags/unmapped)
Fragments: 43566404 total (42332731 tlen-paired, 3524 hash-paired, 341 singletons, 244615 discordant, 985193 orphans, 99261 too large [>5000 bp], 17576911 duplicates)