Why do I get an error message when I run the class I or II binding tools?
The most common reason for run-time errors for the class I and II binding prediction tools is that the data set is too large for the web server to handle. See below for suggested workarounds.
MHC Class I Binding Prediction - “Internal Server Error” (Help request from a user)
User request:
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?
IEDB response:
Our Tools team lead 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.”
MHC II Epitope Prediction - “Internal Server Error” (Help request from a user)
User request:
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."
IEDB response:
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 Tools-API. If you are at a non-profit, you can also download the application and run it on your own computer (MHC-II Download).