I am using CentOS release 6.3 Regards Vidya
On Tue, Jul 10, 2018 at 4:57 PM, David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Which version of linux are you using? I may be able to provide a binary > for you. Or you can recompile from source. > > Cheers, > > -David > > On Tue, Jul 10, 2018 at 4:50 PM, Vidya Venkatraman < > vidya.venk...@gmail.com> wrote: > >> I am using Linux. Do i need to compile it again? >> >> Regards >> >> On Tue, Jul 10, 2018 at 12:07 PM, David Shteynberg < >> david.shteynb...@systemsbiology.org> wrote: >> >>> Hello Vidya, >>> >>> I have added the support of Morpheus into the TPP codebase. Please let >>> me know which OS (windows or linux) you are processing on so I can provide >>> you with an executable that you should be able to use. >>> >>> Thanks, >>> -David >>> >>> On Mon, Jun 25, 2018 at 1:09 PM, Vidya Venkatraman < >>> vidya.venk...@gmail.com> wrote: >>> >>>> I just shared a box folder with you which contains mzML, fasta and the >>>> pepxml file. >>>> >>>> https://cedars.app.box.com/folder/50657299852 >>>> >>>> Regards >>>> Vidya >>>> >>>> On Mon, Jun 25, 2018 at 9:41 AM, David Shteynberg < >>>> david.shteynb...@systemsbiology.org> wrote: >>>> >>>>> Hello Vidya, >>>>> >>>>> Currently, there is no support for Morpheus in the TPP. If you are >>>>> able to place you search results in a shared drive and send me a link for >>>>> testing, I should be able to add the Morpheus support back in. >>>>> >>>>> Thanks, >>>>> -Davod >>>>> >>>>> On Sat, Jun 23, 2018 at 3:25 PM, Vidya Venkatraman < >>>>> vidya.venk...@gmail.com> wrote: >>>>> >>>>>> 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/Pra >>>>>> tik/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> 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_Tut >>>>>>>>> orial_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_D >>>>>>>>>> emo2009/ >>>>>>>>>> >>>>>>>>>> ... 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...@ >>>>>>>>>>>> googlegroups.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/grou >>>>>>>>>>>> ps/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/grou >>>>>>>>>>>> ps/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-discuss+unsubscr...@googlegroups.com. >>>>>> To post to this group, send email to spctools-discuss@googlegroups. >>>>>> com. >>>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "spctools-discuss" group. >>>>> To unsubscribe from this topic, visit https://groups.google.com/d/to >>>>> pic/spctools-discuss/qdmov2KGlJE/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> spctools-discuss+unsubscr...@googlegroups.com. >>>>> To post to this group, send email to spctools-discuss@googlegroups.com >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> 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 post to this group, send email to spctools-discuss@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/qdmov2KGlJE/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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