Hotfix for importing sequence read sets from NCBI

Question: 

During import of a sequence read set as link via its NCBI SRA accession number, I get following error message: Some accession codes could not be found on NCBI (SRA): <SraAccession>: ||||||||400|Unsupported protocol

Answer: 

NCBI recently changed their protocol to check if an accession number exists in their Sequence Read Archive, which results in the above error message and prevents the import as links from NCBI SRA. The import of sequence read sets (SRS) as links from EMBL ENA, Amazon S3 or local file servers is not affected. This issue is resolved in the latest BioNumerics release, which can be obtained from our software download page.

Alternatively, to restore the functionality without the need for administrator rights, you can download a hotfix for this issue.

Proceed as follows to install the hotfix in a BioNumerics database:

  1. Save the hotfix_ncbi_checkaccession.zip file on your hard drive.
  2. Open a BioNumerics database and select File > Install / remove plugins....
  3. In the Plugins dialog box that appears, click on the Database functionality tab.
  4. Press the <Add> button, browse for the hotfix_ncbi_checkaccession.zip file and press <Open>.
  5. Press <Yes> to confirm the addition of a single Python script to the database and <Exit> to close the Plugins dialog box.
  6. Close and re-open the BioNumerics database.

The above procedure should be followed for any database that has the wgMLST client plugin (BioNumerics version 7.5) or the WGS tools plugin (BioNumerics version 7.6) installed and in which you need to import sequence read sets from the NCBI Sequence Read Archive.

Package(s):

Applicable for: 
Version 7.5 - 7.6
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