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:
>
> 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:
>>
>> 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
>>
>>
>>
>>
>> On Fri, Feb 9, 2018 at 12:48 PM, Volkix <xan...@gmail.com> wrote:
>>
>>> 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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>>>>
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