Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/e09f79fe0a1a21147850e4de21008f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/e09f79fe0a1a21147850e4de21008f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_tissue/Sig_18_tissue.recal.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_tissue/Sig_18_tissue.recal.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/shared/somatic_cnv/dbsnp138.snps.hg38.chr21.tsv.gz
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
Loaded 735874 sites across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped), 0 no site overlap
Fragments: 0 total (0 paired, 0 singletons, 0 discordant, 0 orphans)
Loaded 735874 sites across 3366 contigs
Sites: 735874 total, 0 with data, 0 output (depth>=10)
Reads: 9109949 total, 1516 skipped (flags/unmapped), 530821 no site overlap
Fragments: 4732496 total (3845116 paired, 44 singletons, 0 discordant, 887336 orphans)
Sites: 735874 total, 37939 with data, 37491 output (depth>=10)