BUSCO runs to completion, but without gene predictions and no result. Help?

[Genomics101]

Greetings.

I would like to use BUSCO to get an idea of the level of completeness of the eukaryotic genomes I am working on. When I run BUSCO it goes to completion but finds no "BUSCOs." Looking at the results, the BLAST step works fine, but the standard error shows that there are no gb files, no gene predictions, for it to work with. I have installed Augustus and it seems to be in the path (with the config file as well) with no problems.

This happens when I run the test with the sample data that comes with BUSCO the same way as with my actual data.

I am hoping someone else has had this same problem and solved it.

Thanks and all the best.

[maepz]

I have the same problem. Did you solve it?

[lahcen86]

Check the ancestral file

Locate the ancestral file for the particular BUSCO set you are using. I have a feeling you are using Eukaryota, am I right ? I had the same problem with this set. Reporting 0% for all C,D,F,M! Even though my assemblies have returned fairly descent hits for other ortho sets like Arthropod and Metazoa.

Anyway, I noticed that the ancestral file for Eukaryota is distributed from the BUSCO site with incorrect fastA formatting. There are spaces in the single line sequence. This I assume was truncating the sequence used in the BUSCO comparison with HMMER and then obviously not finding a hit as it was drastically too short to meet significance.

So remove those spaces and rerun the analysis, it worked for me !! Good luck