Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/193ca64845ad4384a7b9740758ecf9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/193ca64845ad4384a7b9740758ecf9/.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_Blood/Sig_18_Blood.recalibrated.bam.bai
  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_Blood/Sig_18_Blood.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_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 6313 total, 842 skipped (flags/unmapped), 5471 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: 2446509 total, 989 skipped (flags/unmapped), 300455 no site overlap
Fragments: 1108230 total (1036835 paired, 17 singletons, 0 discordant, 71378 orphans)
Sites: 735874 total, 194290 with data, 62077 output (depth>=10)