X!tandem stops after a few searches

[Volkix]

Hi all,

I have a couple hundreds of raw data to be analyzed. Using the petunia UI, I convert the files into x(z)ml formats without any problems. when it comes to X!tandem search analysis goes for 5-15(at most) files and then stops. Petunia says there is a running job however windows task manager shows no sign of X!tandem as a process. is this a known problem and/or is there a workaround about this.

Best
Volkan

[Luis Mendoza]

Hi Volkan,

This may be a webserver timeout issue; how long do the searches run before they seem to stop?

The easiest workaround is to simply run in batches of 5-10 files.  Another option is to set the webserver timeout to a longer value.  And yet another is to write a script that will do your searches in batch mode, especially if you expect to do this sort of high-volume search regularly.

Are you running on Windows or Linux?

--Luis

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[Volkix]

Hi Luis,

I also thought it is a webserver timeout issue. I tried to increase that value but didn't work. May be I couldn't put correct things in the conf file. Is there any conf file template to avaid server timeout issue.

So I also couldn't install the server on the linux so it is on windows. I think I will try to install tpp on linux without petunia and try to work with batch scripts.
Thank you.
Volkan.

9 Şubat 2018 Cuma 15:29:52 UTC-5 tarihinde Luis yazdı:

Hi Volkan,

This may be a webserver timeout issue; how long do the searches run before they seem to stop?

The easiest workaround is to simply run in batches of 5-10 files.  Another option is to set the webserver timeout to a longer value.  And yet another is to write a script that will do your searches in batch mode, especially if you expect to do this sort of high-volume search regularly.

Are you running on Windows or Linux?

--Luis

On Fri, Feb 9, 2018 at 11:54 AM, Volkix <xan...@gmail.com> wrote:

Hi all,

I have a couple hundreds of raw data to be analyzed. Using the petunia UI, I convert the files into x(z)ml formats without any problems. when it comes to X!tandem search analysis goes for 5-15(at most) files and then stops. Petunia says there is a running job however windows task manager shows no sign of X!tandem as a process. is this a known problem and/or is there a workaround about this.

Best
Volkan

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[Luis Mendoza]

Hi Volkan,

In Windows you will want to edit this file:  C:\TPP\conf\httpd-tpp.conf .

Look for this line, and change the timeout to the desired number of seconds:

Timeout 18000

Please note that you will need to restart the Apache webserver for any changes to take effect.

You could also write batch files for Windows.

As for Linux, which version did you try installing?  We have a page with updated instructions at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.1.0:_Installing_on_Ubuntu_16.04_LTS

It is worth mentioning that the Linux version of the interface is not hampered by the webserver timeout.

Cheers,

--Luis

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[Volkix]

Thank you  Luis;

For the conf file it seems I have confused so I made some tweaking in the apache conf file. So thank you for warning I will try again for timeout change in that file. I also did the apache restart. As for the linux I tried to install on a linux mint 18 with the instructions on the link you suggested as well. Linux Mint is basically an ubuntu variant. But I will give it another shot by installing ubuntu 16.04. I am more comfortable with linux. 

Thank you very much again.

Volkan.

9 Şubat 2018 Cuma 16:33:06 UTC-5 tarihinde Luis yazdı:

[Volkix]

Hi again,

As Luis suggested it turned out to be a server timeout issue and solved as Luis guided. I also installed the ubuntu 16.04 and TPP on it. There is a problem with file permissions so petunia cant reach some folders/files. I didnt want to spend some more time on it and windows works fine right now.

Thanks again.
Volkan.

9 Şubat 2018 Cuma 18:46:58 UTC-5 tarihinde Volkix yazdı:

[Luis Mendoza]

Great!  Thanks for the update and glad that it works.

--Luis

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