Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/33ee8e6ea7897509cb47eacaed395f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/33ee8e6ea7897509cb47eacaed395f/.command.sh
  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_0I-N1-BDNA-1_B23KGCJLT4_1/1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0I-N1-BDNA-1_B23KGCJLT4_1/1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 148143766 total, 96876 skipped (flags/unmapped), 12240422 no site overlap
Fragments: 71151720 total (64611707 paired, 562 singletons, 43041 discordant, 6496410 orphans)
Sites: 53092669 total, 7627672 with data, 3031937 output (depth>=10)
Reads: 161891745 total, 113390 skipped (flags/unmapped), 14220844 no site overlap
Fragments: 77254097 total (70061771 paired, 560 singletons, 241643 discordant, 6950123 orphans)
Sites: 53092669 total, 7226169 with data, 2997514 output (depth>=10)