Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/118caa7a0dd674f0a2841102930a85/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/118caa7a0dd674f0a2841102930a85/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_11H-N1-BDNA-1_B23KGCJLT4_1/1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 213357105 total, 140623 skipped (flags/unmapped), 18515066 no site overlap
Fragments: 102151869 total (92475331 paired, 678 singletons, 74216 discordant, 9601644 orphans)
Sites: 53092669 total, 8350588 with data, 3382219 output (depth>=10)
Reads: 220881029 total, 165282 skipped (flags/unmapped), 18807418 no site overlap
Fragments: 105592782 total (96013815 paired, 722 singletons, 301732 discordant, 9276513 orphans)
Sites: 53092669 total, 7762728 with data, 3223101 output (depth>=10)