Changes made by NCBI in Jan 2018 mean Geneious R11.0.4 or earlier, and Geneious R10.2.3 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.
Users downloading protein sequence results (from blastp or tblastn) may see the error "Download failed - Failed to connect to NCBI server".
Note: This issue has now been fixed in the R10.2.4 and 11.0.5 releases. Users on earlier versions of R10 or R11 should update to restore full NCBI access.
Just go Geneious menu Help -> Check for updates to get a link to the latest update for your version of Geneious.
This issue will not be fixed for older unsupported versions of Geneious (R9 and earlier).
Note that users 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.