Hotfix for importing sequence read sets from NCBI


During import of a sequence read set as link via its NCBI SRA accession number, I get a “file not found” (HTTP 404) error.


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.

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 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 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 WGS tools plugin (referred to as wgMLST client plugin in BioNumerics version 7.5) installed and in which you need to import sequence read sets from the NCBI Sequence Read Archive.

Applicable for: 
Version 7.5 - 8.0