Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/a19d3cf43cfad1d990c485320ec569/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/a19d3cf43cfad1d990c485320ec569/.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_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-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_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 226167001 total, 141393 skipped (flags/unmapped), 19060797 no site overlap
Fragments: 108992327 total (97917056 paired, 749 singletons, 55428 discordant, 11019094 orphans)
Sites: 53092669 total, 8455238 with data, 3544927 output (depth>=10)
Reads: 243105212 total, 163906 skipped (flags/unmapped), 21773973 no site overlap
Fragments: 116319359 total (104455931 paired, 847 singletons, 392043 discordant, 11470538 orphans)
Sites: 53092669 total, 7969259 with data, 3434027 output (depth>=10)