Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_D92-N1-BDNA-1_A23KFG7LT4_1/1029_D92-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/d08a2ead38ccea16c9cfb0c2c04381/.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/3e/d08a2ead38ccea16c9cfb0c2c04381/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_D92-N1-BDNA-1_A23KFG7LT4_1/1029_D92-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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_D92-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D92-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D92-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D92-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: 58958183 total, 42884 skipped (flags/unmapped)
Fragments: 29648294 total (29236152 tlen-paired, 2126 hash-paired, 324 singletons, 11311 discordant, 398381 orphans, 8708 too large [>5000 bp], 11092080 duplicates)
Reads: 63171877 total, 36163 skipped (flags/unmapped)
Fragments: 31770269 total (31340754 tlen-paired, 1511 hash-paired, 413 singletons, 8008 discordant, 419583 orphans, 7586 too large [>5000 bp], 11513270 duplicates)
Reads: 69211002 total, 40203 skipped (flags/unmapped)
Fragments: 34807907 total (34309582 tlen-paired, 2725 hash-paired, 311 singletons, 12391 discordant, 482898 orphans, 19097 too large [>5000 bp], 12996589 duplicates)
Reads: 70619881 total, 67012 skipped (flags/unmapped)
Fragments: 35716166 total (34335258 tlen-paired, 2596 hash-paired, 354 singletons, 273757 discordant, 1104201 orphans, 112546 too large [>5000 bp], 13263488 duplicates)