Recent changes made by NCBI mean Geneious 11.0.4 or earlier can no longer download sequences from NCBI Genomes and Nucleotide.
The Error "Download failed -Unexpected end of file null" is returned when users try to download a full search result.
Note: This issue has now been fixed in the 11.0.5 release. A fix for Geneious R10 will be released in February.
For users who do not update to Geneious R10.2.4 (available in February) or R11.0.5 or later, you can still download sequences from the NCBI website using the Accession numbers returned from your NCBI search.
For example, if search results returned a sequence of interest, right click on the entry and go Copy name (this is also the sequence Accession number).
Go to https://www.ncbi.nlm.nih.gov/ and search for the Accession number.
Follow the link to the appropriate sequence, and go Send To -> File -> GenBank (full).
This will download the GenBank file to your computer. Drag and drop the GenBank file into the Geneious Sources panel to import it into Geneious.