Due to a recent hardware failure in the CPT’s Apollo system, some Apollo organism data were corrupted. These organisms are not viewable in Apollo (error message “Could not load reference sequence definitions”) and cannot be retrieved into Galaxy by the normal mechanism of the Retrieve Data tool.
However, these organisms and their annotations can be retrieved from Apollo with a new Galaxy tool called Retrieve Data Fix (here). When running this tool, select the desired organism to retrieve AND provide the FASTA DNA sequence of the organism (e.g., the FASTA dataset used to create the organism in the initial run of the Structural Workflow). This will allow the tool to rebuild the GFF3 annotations and place them in your history. The dataset can then be downloaded as normal.