nan detected in NonParametricDistribution ... TPP Kojak

[Alex Zelter]

I'm running into the following error when trying to use xinteract to process Kojak 2.0 results. 

The command I'm running is:

/usr/local/tpp/bin/xinteract -Ninteract.pep.xml -p0 -l1 -eT -D/path/to/database.fasta -PPM -OAPdp -drandom_ -ip ./kojak-output.pep.xml

INFO: Processing xl MixtureModel ...

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201908090730-7945 (Linux-x86_64)) AKeller@ISB

 read in 0 1+, 34 2+, 11290 3+, 7625 4+, 2948 5+, 874 6+, and 13 7+ spectra.

Initialising statistical models ...

Found 13541 Decoys, and 9243 Non-Decoys

Iterations: DEBUG HERE ...

ERROR: nan detected in NonParametricDistribution ...

command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' MINPROB=0 PPM ACCMASS NONPARAM DECOYPROBS DECOY=random_" exited with non-zero exit code: 256

QUIT - the job is incomplete

This was previously working for me using TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build 201809101205-7809 (Linux-x86_64))

INFO: Processing xl MixtureModel ...

 PeptideProphet  (TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build 201809101205-7809 (Linux-x86_64)) AKeller@ISB

 read in 0 1+, 34 2+, 11290 3+, 7625 4+, 2948 5+, 874 6+, and 13 7+ spectra.

Initialising statistical models ...

Found 13541 Decoys, and 9243 Non-Decoys

Iterations: .........10.........20......

WARNING: Mixture model quality test failed for charge (1+).

WARNING: Mixture model quality test failed for charge (2+).

WARNING: Mixture model quality test failed for charge (7+).

model complete after 27 iterations

INFO: Processing loop MixtureModel ...

etc. 

If anyone has any ideas why I am running into this error with the new build I'd be very grateful!

Thanks!

Alex

[David Shteynberg]

Hi Alex,

It looks like you are running an unofficial version of the code that obviously has a few issues with this data and has aged by this point.  If you can share your input data I can try the latest version of the code and see if that works or provide a solution in the near future?

Cheers,

-David

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[David Shteynberg]

Hi Alex,

Thanks for sharing your file.  I have confirmed that the latest version of the code (SVN revision 8004) has corrected this problem.  Please update your TPP software to latest SVN revision (or official release.)

Cheers,

David

On Tue, Jan 28, 2020 at 8:57 AM Alex Zelter <aze...@uw.edu> wrote:

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[Alex Zelter]

Hi David,

Thanks very much for looking at this so quickly. I checked out the latest build, TPP v5.2.1-dev Flammagenitus, Build 202001280920-8004, and that has resolved the issue.

Cheers,

Alex

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