Hi David, I am using TPP v5.1.0 and when i try to run xinteract on the Morpheus pep.xml, I get the following error that engine Morpheus not recognized. Any ideas if I am missing something?
xinteract (TPP v5.1.0 Syzygy, Build 201806211802-exported (Linux-x86_64)) running: "/hpc/apps/TPP/5.1.0/bin/InteractParser 'interact.morpheus.pep.xml' '2017-12-4_ABRF_200_DDA1.pep.xml' -L'7'" file 1: 2017-12-4_ABRF_200_DDA1.pep.xml processed altogether 72135 results command completed in 9 sec running: "/hpc/apps/TPP/5.1.0/bin/DatabaseParser 'interact.morpheus.pep.xml'" command completed in 1 sec running: "/hpc/apps/TPP/5.1.0/bin/RefreshParser 'interact.morpheus.pep.xml' '/common/venkatramanv/Data/Pratik/Thermo/DDA/raw/PRG2016_DECOY.fasta'" - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 15 sec running: "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" using Accurate Mass Bins using RT Using Decoy Label "DECOY_". Decoy Probabilities will be reported. Using non-parametric distributions (Morpheus) error: engine Morpheus not recognized command "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" exited with non-zero exit code: 256 QUIT - the job is incomplete Thanks Vidya On Friday, February 7, 2014 at 12:22:54 PM UTC-8, David Shteynberg wrote: > > I was able to make a first stab attempt at it and I was successful after > minor modification to the way spectrum_names are encoded in spectrum_query > tags in the morpheus pepXML files. After running a simple sed to replace > the names with something that wouldn't overlap with anoth file when > combined by using the each run's basename I was able to generate results. > > > My PeptideProphet processed analysis for these two searches can be > downloaded here: > > https://www.dropbox.com/s/f5r8j5yj2p2r3b8/morpheus_interact.tgz > > > Here are my sed commands, but I hope this could be fixed within morpheus. > > sed -i 's/controllerType=0 controllerNumber=1 > scan=[0-9]*/OR20080317_S_SILAC-LH_1-1_01/g' > OR20080317_S_SILAC-LH_1-1_01.pep.xml > > > sed -i 's/controllerType=0 controllerNumber=1 > scan=[0-9]*/OR20080320_S_SILAC-LH_1-1_11/g' > OR20080320_S_SILAC-LH_1-1_11.pep.xml > > > > Cheers, > -David > > > P.S. I expect to merge this into the SVN codebase sooner than later. > > > > > On Fri, Feb 7, 2014 at 8:35 AM, Dave Trudgian < > david.t...@utsouthwestern.edu <javascript:>> wrote: > >> David, >> >> That's the same data. I've made PepXML and the other Morpheus output >> available at: >> >> https://proteomics.swmed.edu/data/morpheus_tpp/ >> >> DT >> >> >> On Thursday, February 6, 2014 5:36:35 PM UTC-6, David Shteynberg wrote: >> >>> I was referring to this data: >>> >>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial_v2 >>> >>> However, this is not high res MS/MS either. This would be a good >>> starting point. The decoys and targets don't have to separate by score >>> alone, PeptideProphet should be able to model the plots you show in either >>> case. >>> >>> Cheers, >>> -David >>> >>> >>> On Thu, Feb 6, 2014 at 3:13 PM, Dave Trudgian <david.t...@ >>> utsouthwestern.edu> wrote: >>> >>>> Hi David, >>>> >>>> Am happy to generate some pepXMLs from the tutorial data, but assuming >>>> you mean the stuff at: >>>> >>>> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/TPP_Demo2009/ >>>> >>>> ... I'm not sure that's the best to work with for Morpheus. It's CID >>>> Ion-trap MS/MS, which is not Morpheus' target. Morpheus doesn't work as >>>> well as other algorithms on low-res MS/MS so I'm not sure if anyone would >>>> want to use it like that. >>>> >>>> I grabbed two of the result sets from the Coon lab site - Yeast >>>> analysis with FT HCD or IT CID. The distributions of Morpheus scores are >>>> very different. The CID data doesn't even look like target and decoy >>>> matches are separable, so I think high-res MS/MS is a must. See attached. >>>> >>>> DT >>>> >>>> >>>> On Thursday, February 6, 2014 3:44:08 PM UTC-6, David Shteynberg wrote: >>>> >>>>> I was dabbling in this, but running into some issues with morpheus >>>>> slowing my machine to a point where I was unable to do any other work so >>>>> I >>>>> moved to another project. However, I am certainly still interested in >>>>> this, but I know that pepXML coming out of morpheus may need some work. >>>>> If >>>>> you'd be willing to generate some pepXML's from the tutorial data and >>>>> work >>>>> with me to correct the pepXML issues I should be able to model the >>>>> results >>>>> quite quickly with PeptideProphet. Please let me know if that sounds >>>>> good >>>>> to you. >>>>> >>>>> Cheers, >>>>> -David >>>>> >>>>> >>>>> On Thu, Feb 6, 2014 at 12:08 PM, Eric Deutsch < >>>>> edeu...@systemsbiology.org> wrote: >>>>> >>>>>> Hi Dave, at ISB we are not planning this, so please go ahead and let >>>>>> us know how it goes! >>>>>> >>>>>> >>>>>> >>>>>> Regards, >>>>>> >>>>>> Eric >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> *From:* spctools...@googlegroups.com [mailto:spctools...@googlegrou >>>>>> ps.com] *On Behalf Of *Dave Trudgian >>>>>> >>>>>> *Sent:* Thursday, February 06, 2014 12:02 PM >>>>>> *To:* spctools...@googlegroups.com >>>>>> >>>>>> *Subject:* [spctools-discuss] Re: support for Morpheus search >>>>>> algorithm in TPP >>>>>> >>>>>> >>>>>> >>>>>> Craig, just wondering if you or anyone else is working on this? If >>>>>> not I was thinking I would have a go at putting in a Morpheus model for >>>>>> PeptideProphet towards the end of next week. >>>>>> >>>>>> >>>>>> >>>>>> Dave Trudgian >>>>>> >>>>>> On Saturday, November 30, 2013 4:37:30 PM UTC-6, Craig Wenger wrote: >>>>>> >>>>>> Is there a mechanism for adding support for a new search algorithm to >>>>>> the various TPP tools? A few users have requested TPP compatibility for >>>>>> the >>>>>> Morpheus <http://morpheus-ms.sourceforge.net/> search algorithm. It >>>>>> already outputs pepXML. >>>>>> >>>>>> >>>>>> >>>>>> -Craig >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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-discu...@googlegroups.com. >>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>> >>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>>> -- >>>>>> 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-discu...@googlegroups.com. >>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>> >>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>> >>>>> -- >>>> 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-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >> 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-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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