Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_16G-T1-TDNA-1_B23KFCWLT4_1/1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/caeed467d7e8cecb425d2af93494fc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_16G-T1-TDNA-1_B23KFCWLT4_1/1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/caeed467d7e8cecb425d2af93494fc/.command.run
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 669999667 total, 2151673 skipped (flags/unmapped), 54159605 no site overlap
Fragments: 318608399 total (294370495 paired, 2838 singletons, 709495 discordant, 23525571 orphans)
Sites: 53092669 total, 10293174 with data, 4944108 output (depth>=10)
Reads: 713255515 total, 2080875 skipped (flags/unmapped), 62091472 no site overlap
Fragments: 336723576 total (311246197 paired, 3140 singletons, 1113395 discordant, 24360844 orphans)
Sites: 53092669 total, 9604881 with data, 4679142 output (depth>=10)