Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/96925859b0e5a3ca3a896abb3e0862/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dc8-N1-BDNA-1_B23KFG5LT4_1/659_dc8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/5e/96925859b0e5a3ca3a896abb3e0862/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dc8-N1-BDNA-1_B23KFG5LT4_1/659_dc8-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: 659_dc8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dc8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dc8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dc8-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: 97546458 total, 57308 skipped (flags/unmapped)
Fragments: 48901322 total (48546176 tlen-paired, 2744 hash-paired, 496 singletons, 15052 discordant, 336854 orphans, 11928 too large [>5000 bp], 19876845 duplicates)
Reads: 90937779 total, 70353 skipped (flags/unmapped)
Fragments: 45585834 total (45233392 tlen-paired, 3369 hash-paired, 469 singletons, 21397 discordant, 327207 orphans, 11717 too large [>5000 bp], 18929294 duplicates)
Reads: 97383070 total, 63512 skipped (flags/unmapped)
Fragments: 48824827 total (48426350 tlen-paired, 5115 hash-paired, 416 singletons, 18350 discordant, 374596 orphans, 22458 too large [>5000 bp], 20363200 duplicates)
Reads: 107965862 total, 103079 skipped (flags/unmapped)
Fragments: 54215818 total (53333149 tlen-paired, 3115 hash-paired, 452 singletons, 168379 discordant, 710723 orphans, 71161 too large [>5000 bp], 22621932 duplicates)