Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['Luis Mendoza' via spctools-discuss]

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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[spctools-discuss] Re: TPP 5.2.0 installation error CentOS 7.8

[Wenhao]

Anyway, I have solve this problem by using Docker based on Ubuntu 16.04. I 
suppose it is a dependency problem.

在2020年10月8日星期四 UTC+8 下午12:34:06 写道：

> Hi,
>
> I am trying to install TPP 5.2.0 on CentOS Linux release 7.8.2003.
>
> After compiling without error, I executed the command ```make install```. 
> Then an error occurred as ```make: *** No rule to make target 
> `/usr/local/tpp/lib/Mayu/BinnedEntity.pm', needed by `install'.  Stop.```
>
> Is this due to a lack of prerequisite software? By the way, the folder 
> "/usr/local/tpp/lib" is not existed under "tpp", is this normal?
>
> Looking forward to your reply.
>
> Best regards,
> Wenhao
>

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