MHC class I binding prediction - Internal Server Error

Question (Originally from ticket #1982)

I am getting this error message every time I try to perform MHC I binding predictions.

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

I am querying a 100 sequence file (51 Kb) against 27 HLA alleles using SMM (in Google Chrome).
Do you have any suggestions?

Answer:

Our bioinformatics core manager has provided the following response, which includes guidelines for configuring your runs:

"The issue is that this is simply too large of a data set for the web server to handle currently. There are over 45K 9mers in the data set and 30 allele-length combinations, corresponding to well over 1.3 million predictions being performed. We are addressing this issue by smart parallelization in the background, but that will not be deployed until later this year. In the meantime, I would suggest the user either use the standalone tools or breaks up the data set into smaller chunks. As a general guideline, I would suggest performing no more than 20K predictions (nmers x allele-length combinations) at a time, particularly for netMHCpan, which is very CPU-intensive."