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

['David Shteynberg' via spctools-discuss]

Hello,

Generally this message means that you have no PSMs with good likelihoods of
being correct in this analysis set.
There are a few "usual suspect" reasons for why you would not observe any
PSMs with non-zero probabilities among your results.

1. Poor quality data (e.g. empty sample)

2. Incorrect database (e.g. wrong organism, common contaminants missing)

3. Incorrect search parameters (e.g. wrong tolerances or incorrect static
modifications specified)

Please go down the list to help yourself troubleshoot.

-David





On Tue, Nov 29, 2022 at 4:34 PM 'Luis Mendoza' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> 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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>> "spctools-discuss" group.
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>> https://groups.google.com/d/msgid/spctools-discuss/1a4f392c-7ec1-411b-8300-90c0f6b48158n%40googlegroups.com
>> 
>> .
>>
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> .
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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
>
> --
> 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-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/1a4f392c-7ec1-411b-8300-90c0f6b48158n%40googlegroups.com
> 
> .
>

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