Re: [spctools-discuss] protein prophet failing on Eclipse searches

['Luis Mendoza' via spctools-discuss]

Hi,
Congrats on the new instrument, and happy holidays as well!

The error seems to indicate that there is no input data for ProteinProphet
to work with; can you verify that the input file contains validated search
results with probabilities above 0.2 ?  Are there any other errors or
warnings in the previous steps?

Feel free to directly send me the interact.pep.xml file and I can have a
look as well.

Cheers,
--Luis


On Tue, Nov 29, 2022 at 10:31 AM cabarnes...@gmail.com <
cabarnescabar...@gmail.com> wrote:

> Hi all,
>
> Happy holidays!  I have a new Eclipse in the lab and have been running my
> Comet + TPP pipeline successfully on a lot of data downloaded from PRIDE
> lately, but have run into an error with the new DDA data generated on the
> Eclipse.  It seems to be failing at the protein prophet step and the error
> doesn't make much sense to me.  Any idea what is going on?
>
> I'm running TPP 6.1 and Comet 2022.01 rev. 1 although the error below is
> from the output of the Comet search through the TPP interface.  I get a
> similar error on the command line at the same step.
>
>
> Here's the error message:
>
> WARNING: no data - output file will be empty
>
> command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml""
> failed: Operation not permitted
>
> command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml""
> exited with non-zero exit code: 1
> QUIT - the job is incomplete
>
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> 
> .
>

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[spctools-discuss] protein prophet failing on Eclipse searches

[cabarnes...@gmail.com]

Hi all,

Happy holidays!  I have a new Eclipse in the lab and have been running my 
Comet + TPP pipeline successfully on a lot of data downloaded from PRIDE 
lately, but have run into an error with the new DDA data generated on the 
Eclipse.  It seems to be failing at the protein prophet step and the error 
doesn't make much sense to me.  Any idea what is going on?

I'm running TPP 6.1 and Comet 2022.01 rev. 1 although the error below is 
from the output of the Comet search through the TPP interface.  I get a 
similar error on the command line at the same step.  


Here's the error message:

WARNING: no data - output file will be empty

command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml"" 
failed: Operation not permitted

command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml"" 
exited with non-zero exit code: 1
QUIT - the job is incomplete

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