1.1. Why isn't my Genbank file accepted for import?
The CLC Workbenches accept standard Genbank format files, such as those you can obtain from the Genbank repository.
We are aware that some third party software tools generate Genbank format files that not entirely standard, and when this occurs, such files may not be recognized as Genbank files by the CLC Workbenches. Examples of issues we have seen in the past, and thus which could be worth checking in Genbank files you have been unable to import, include
- non-standard Locus lines (e.g. Locus lines where identifiers have spaces in them)
- inclusion of non-standard characters in annotations
- missing SOURCE or ORGANISM fields
- badly formatted feature entries. Examples we have seen include feature entries without a name, feature names that run straight into the region with no tab between, and standard qualifiers grouped under non-standard qualifiers put in by third party software.
In at least one piece of software we are aware of, there was an option in the preferences for "strict Genbank" format to be used. That caused the formatting used to adhere to the Genbank format and those files could be imported into the Workbench. If the software you are using offers such an option or feature, then turning that on may be worth trying.
The Gebank/EMBL/DDBJ feature definition can be found online at:
If you are confident that your file is in valid Genbank format and you are still experiencing problems importing it into a CLC Workbench, and you are eligible for support from us, then please contact the Support team by emailing firstname.lastname@example.org. Attaching a copy of your Genbank file to your email may help us troubleshoot the issue.