Issue

In August 2025, snpEff moved the hosting location of its caches (SnpEff#602). snpEff versions older than 5.3 still point to the old location, so downloading a cache with --download_cache fails with an error such as:

FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/...

In addition, cache version 105 no longer exists in snpEff and cannot be resolved (SnpEff#609). The affected pipeline versions use version 105 by default for GRCh38, R64-1-1 and WBcel235.

Affected versions, when run with --download_cache:

• sarek 3.2.0 to 3.5.1
• rnavar 1.1.0 to 1.2.1

Runs that use the default annotation cache or a cache you downloaded yourself are not affected.

Resolution

Update to sarek 3.6.0 or later, or rnavar 1.2.2 or later. These versions use snpEff 5.3 and default to cache version 99 instead of 105.

Do not use cache version 105 with these versions: use version 99 or earlier (for example --snpeff_db GRCh38.99).