Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

Hello Emily,

If you are able to share the dataset including the pepXML file and the
database I can try to replicate the issue here and try to troubleshoot the
sticking point.

Thanks,
-David

On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler  wrote:

> Hello, and thank you for your response! It doesn't look like the process
> is using too much memory (I've allocated 300 GB and it's maxing out around
> 10), and I've kicked up the minprob parameter - it's still getting stuck,
> unfortunately.
> Emily
>
> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>
>> Hello Emily,
>>
>> This is not a problem that we have seen much of.  Do you know which
>> version of ProteinProphet / TPP you are using?
>>
>> One potential issue is the large number of proteins (and peptides) that
>> it is trying to process -- can you either monitor the memory usage of the
>> machine when you run this dataset, and/or try on one with more memory?
>>
>> Hope this helps,
>> --Luis
>>
>>
>> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler  wrote:
>>
>>> Hello! I've been running ProteinProphet as part of the Philosopher
>>> pipeline for a while now with no problems. However, one of my datasets
>>> seems to be getting stuck in the middle of this function. It doesn't throw
>>> an error or anything - just stops advancing (the last
>>> line of the output is "Computing degenerate peptides for 69919 proteins:
>>> 0%...10%...20%...30%...40%...50%"). Has anyone run into this problem before?
>>>
>>> --
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>>> 
>>> .
>>>
>> --
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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Hello, and thank you for your response! It doesn't look like the process is 
using too much memory (I've allocated 300 GB and it's maxing out around 
10), and I've kicked up the minprob parameter - it's still getting stuck, 
unfortunately. 
Emily

On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:

> Hello Emily,
>
> This is not a problem that we have seen much of.  Do you know which 
> version of ProteinProphet / TPP you are using?
>
> One potential issue is the large number of proteins (and peptides) that it 
> is trying to process -- can you either monitor the memory usage of the 
> machine when you run this dataset, and/or try on one with more memory?
>
> Hope this helps,
> --Luis
>
>
> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler  wrote:
>
>> Hello! I've been running ProteinProphet as part of the Philosopher 
>> pipeline for a while now with no problems. However, one of my datasets 
>> seems to be getting stuck in the middle of this function. It doesn't throw 
>> an error or anything - just stops advancing (the last 
>> line of the output is "Computing degenerate peptides for 69919 proteins: 
>> 0%...10%...20%...30%...40%...50%"). Has anyone run into this problem before?
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>>  
>> 
>> .
>>
>

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