MHC II Epitope Prediction - "Internal Server Error"

Question (9 Oct 2015 - ticket #1986):

Hello, I have tried to use the MHC II epitope prediction tool 4-5x using the attached file.

I am using the IEDB recommended prediction method, Human, HLA-DR species, and HLA allele reference set. Output specifications I left as the default. Each time I've submitted the request I see "Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at webmaster@localhost to inform them of the time this error occurred, and the actions you performed just before this error.

More information about this error may be available in the server error log." within 15 minutes. Please help.

Answer:

Thanks for your inquiry. The problem is that our server cannot handle the number of allele/lengths and the numerous protein sequences in one run. We are currently working to speed up the application, which will help in the future. For the time being, I recommend running one protein sequence at a time for your given set of alleles/lengths. I just tried the run for the first protein in your FASTA file and it ran successfully. The output format defaults to text instead of html when there are more than 10,000 records, which is the case here. You can also consider running the code using the API available at http://tools.iedb.org/main/tools-api/. If you are at a non-profit, you can also download the application and run it on your own computer (http://tools.iedb.org/mhcii/download/).