sarek icon indicating copy to clipboard operation
sarek copied to clipboard

Snpeff databases can not be downloaded

Open Proton-NTA opened this issue 3 months ago • 1 comments

Description of the bug

As Microsoft no longer provides the snpeff databases the download of the databases throws an error.

According to this issue the newer version 5.3 of snpeff can download the databases correctly.

Command used and terminal output

Caused by:
  Process `NFCORE_SAREK:DOWNLOAD_CACHE_SNPEFF_VEP:SNPEFF_DOWNLOAD (GRCh38.105)` terminated with an error exit status (255)


Command executed:

  snpEff \
      -Xmx28800M \
      download GRCh38.105 \
      -dataDir ${PWD}/snpeff_cache \
  
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:DOWNLOAD_CACHE_SNPEFF_VEP:SNPEFF_DOWNLOAD":
      snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.105.zip
  00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.105.zip
  FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.105.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.105.zip]

Relevant files

No response

System information

No response

Proton-NTA avatar Sep 11 '25 11:09 Proton-NTA

I don't see 5.3 as a release on github or on bioconda yet unfortunately

maxulysse avatar Sep 11 '25 11:09 maxulysse