Unable to do PeptideProphet in bulk

[Kate Mostovenko]

Hi all,

Maybe somebody had a similar problem, I tried to research the group for it but couldn't find the solution. I have 93 pep.xml files (result of X!Tandem search) and I try to run xinteract via command line. Unfortunately, the process gets terminated on the stage of InteractParser with the error:

This application has requested the Runtime to terminate it in an unusual way.

Please contact the application's support team for more information.

When I split the data in two parts of 36 and 57 files, xinteract works totally fine on both subsets, saying that files are not corrupted or there is nothing wrong with them. It doesn't matter what order the files go (I did reorder them) it seems that it is not going any further than 74 files.

Did anyone encounter similar problem and maybe knows how to deal with it?

I have a latest version (4.7) of TPP and increased to 24h timeout in Apache.

Thank you,

Kate

[Magnus....@gmail.com]

Hi Kate,

The Apache timeout should not matter if you run in from the command line. Are the file names very long? You may have an 8192-character limit on the entire command...


Cheers,

Magnus

[Kate Mostovenko]

Hi Magnus,

I know there is an issue with that but the file names are relatively short adding up in total to less than 2500 characters. I'll truncate them though anyways and see if that helps.

Thanks,

Kate

[Luis Mendoza]

Hi Kate,

Were you able to resolve this?  Are you doing this on a Windows or Linux installation?  Some older Windows systems have a file size limit of 4GB -- perhaps you could be reaching this?

Cheers,

--Luis

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[Kate Mostovenko]

Hi Luis,

Unfortunately, I was not able to process all the files at once and was forced to do it in parts. I have Windows 7 and none of the files exceeded 4GB, the total that I was able to process was 6GB (63 files). Are there any other limitations?

Cheers,

Kate

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