Re: [spctools-discuss] Re: TPP Comet search time-out

['David Shteynberg' via 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:

https://groups.google.com/g/spctools-discuss/c/ZNXMkdB9Y48/m/TYcnPIHgBwAJ

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)

Cheers,
-David

On Thu, Dec 16, 2021 at 8:20 AM Will Comstock  wrote:

> 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.
>
> -Will
>
> On Wednesday, November 10, 2021 at 1:32:09 AM UTC-5 steven...@gmail.com
> wrote:
>
>> 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
>> Steven
>>
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> 
> .
>

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Re: [spctools-discuss] Re: TPP Comet search time-out

[Fahad Saeed]

Use HiCOPS: Will run till the end of time and fast
https://hicops.github.io/



On Thu, Dec 16, 2021 at 11:20 AM Will Comstock  wrote:

> 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.
>
> -Will
>
> On Wednesday, November 10, 2021 at 1:32:09 AM UTC-5 steven...@gmail.com
> wrote:
>
>> 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
>> Steven
>>
> --
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> "spctools-discuss" group.
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> 
> .
>

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[spctools-discuss] Re: TPP Comet search time-out

[Will Comstock]

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.

-Will

On Wednesday, November 10, 2021 at 1:32:09 AM UTC-5 steven...@gmail.com 
wrote:

> 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
> Steven
>

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