Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0W2-N1-BDNA-1_B23KGCJLT4_1/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/0bdaa8816ed8bdbbb09423b75d57fc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/0bdaa8816ed8bdbbb09423b75d57fc/.command.run
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0W2-N1-BDNA-1_B23KGCJLT4_1/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 141324826 total, 104193 skipped (flags/unmapped), 12094818 no site overlap
Fragments: 68057070 total (61040171 paired, 558 singletons, 28574 discordant, 6987767 orphans)
Sites: 53092669 total, 7569672 with data, 3094447 output (depth>=10)
Reads: 155201738 total, 128287 skipped (flags/unmapped), 14502954 no site overlap
Fragments: 74062083 total (66232368 paired, 586 singletons, 276046 discordant, 7553083 orphans)
Sites: 53092669 total, 7185355 with data, 3075530 output (depth>=10)