Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/0753766de555d06c1281ff55b250a8/.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/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/0753766de555d06c1281ff55b250a8/.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/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  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: HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
Loaded 735874 sites across 3366 contigs
Loaded 735874 sites across 3366 contigs
Reads: 4797 total, 663 skipped (flags/unmapped), 4134 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: 1927049 total, 991 skipped (flags/unmapped), 255051 no site overlap
Fragments: 862358 total (808649 paired, 15 singletons, 0 discordant, 53694 orphans)
Sites: 735874 total, 174387 with data, 55783 output (depth>=10)