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 On Tue, Jan 28, 2020 at 8:57 AM Alex Zelter <[email protected]> wrote: > 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 > > -- > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/5436d7d4-3810-4af0-b32d-c432ebd91c5e%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/5436d7d4-3810-4af0-b32d-c432ebd91c5e%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_2nREY2yz4KH-tDfL89sZ9iknYeZ9vOJjOifrzCcg5Uw%40mail.gmail.com.
