Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_tumor/HCC1395_tumor.recal.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/5d15d93d6630345fef7aa602e9702f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/5d15d93d6630345fef7aa602e9702f/.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/HCC1395_tumor/HCC1395_tumor.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: HCC1395_tumor.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.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: 3618686 total, 765 skipped (flags/unmapped), 219919 no site overlap
Fragments: 1960378 total (1437624 paired, 18 singletons, 0 discordant, 522736 orphans)
Sites: 735874 total, 37843 with data, 37072 output (depth>=10)