Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/65fe7dd8e20e396d37d9c6a93e0cc7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/65fe7dd8e20e396d37d9c6a93e0cc7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/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.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 45689 total, 6170 skipped (flags/unmapped), 39519 no site overlap
Fragments: 0 total (0 paired, 0 singletons, 0 discordant, 0 orphans)
Sites: 735874 total, 0 with data, 0 output (depth>=10)
Reads: 12153017 total, 10381 skipped (flags/unmapped), 1413852 no site overlap
Fragments: 5495081 total (5233703 paired, 57 singletons, 0 discordant, 261321 orphans)
Sites: 735874 total, 275497 with data, 98384 output (depth>=10)