TPP Comet search time-out

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Steven He

Nov 10, 2021, 1:32:09 AM11/10/21
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Hi everyone,

I've been using TPP for a little while now for the analysis of my data. I have been using Comet to perform database searching on a large number of mzml files and have noticed that the analysis will usually time out after about 6 hours. In this case, I will remove the mzml files that have been successfully processed and then re-run comet. Is this job time-out an inherent part of TPP, or is it a setting that can be changed? If the latter, are there any risks in running the analysis for over 6 hours?

Thanks in advance for any advice

Will Comstock

Dec 16, 2021, 11:20:49 AM12/16/21
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I have also been encountering this issue and would love to hear a solution. The search still reads as "Running" but simply stops searching any more mzML files. Depending on the size of my  files, the search times out at different points, but will almost never search more than 8 files at a time. 

Happy to provide an example dataset + parameters + FASTA file if anyone wants to try and replicate the timeout.


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David Shteynberg

Dec 16, 2021, 3:13:00 PM12/16/21
to spctools-discuss
Hi Will,

Thanks for posting your question.  
This is due to a timeout setting in the webserver.  Thankfully there is a simple fix:

In Windows the steps are :

1. Edit this file:  C:\TPP\conf\httpd-tpp.conf .

2. Change the timeout to a large number of seconds:

     Timeout 864000

(this will set the timeout to 10 days!)

3. Restart the Apache webserver (you can also find it in Services)


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