Sure. I am not completely sure that my fix is correct. Under two functions:
NonParametricDistribution::densityFit NonParametricDistribution::varBWdensityFit I changed : (*d)[i] = (*d)[i] / k->size(); into: if ( k->size() == 0) (*d)[i] = 0; else (*d)[i] = (*d)[i] / k->size(); That is where I got the NAN error at the first point. Thanks, Ping On Jul 14, 8:46 am, GATTACA <[email protected]> wrote: > Ping, > > Could you post what changes you made to the > NonParametricDistribution.cxx to fix the NAN error? > > Thanks. > > On Jul 9, 1:21 pm, Ping <[email protected]> wrote: > > > Jimmy, > > > Thanks for your information. > > > I debug the TPP source code. There is a small bug inside the > > NonParametricDistribution.cxx which causes theNANerror in the > > previous tries. I fix it and the PeptideProphetParser is working fine > > now. > > > Also after enabling InteractParser option -P as Davis suggested, I do > > not need to replace the value in the "protein" with the first word > > from the "protein_descr" in each search_hit entry. > > > Thanks again, > > > Ping > > > On Jul 6, 1:55 pm, Jimmy Eng <[email protected]> wrote: > > > > Has anyone been able to feedOMSSAnative pepXML output (using -op > > > option) through PeptideProphet? I don't know if anyone has tested this > > > or ifOMSSAhas only been tested using a separate converter. > > > > Replacing the protein word was to address the error message having no > > > DECOY entries. This fix hopefully addressed that one point which is > > > seems to have done. So to address the follow-up problem, minimally > > > you'll want to include the diagnostic output from PeptideProphetParser > > > in case anything obvious shows up from that info. Possibly you'll need > > > to have a developer, who knows more than I do, take a closer look at > > > your data. > > > > - Jimmy > > > > Ping wrote: > > > > Jimmy, > > > > > As you suggested, I replace the value in the "protein" with the first > > > > word from the "protein_descr" in each search_hit entry. But when I run > > > > PeptideProphetParser, it still gives the error message: > > > > > ERROR:NANprobability density detected. Please alert the > > > > developer !!! > > > > > Is there anything else I need to fix? > > > > > Thanks! > > > > > Ping > > > > > Here is the example of the result after I replace protein/ > > > > protein_descr > > > > > for not decoy string, it looks like this: > > > > > <search_hit hit_rank="1" peptide="YPSRPLPPPPPFGLGFVPPPPPPYGPGR" > > > > peptide_prev_aa="R" peptide_next_aa="I" protein="gi|73975149|ref| > > > > XP_862242.1|" num_tot_proteins="3" num_matched_ions="15" > > > > tot_num_ions="54" calc_neutral_pep_mass="2949.569" > > > > massdiff="0.59985990298992" is_rejected="0" protein_descr="gi| > > > > 73975149| > > > > ref|XP_862242.1| PREDICTED: hypothetical protein XP_857149 isoform 2 > > > > [Canis familiaris]" num_tol_term="2" num_missed_cleavages="0"> > > > > <alternative_protein protein="gi|73975151|ref|XP_862273.1|" > > > > protein_descr="gi|73975151|ref|XP_862273.1| PREDICTED: hypothetical > > > > protein XP_857180 isoform 3 [Canis familiaris]"/> > > > > <alternative_protein protein="gi|73975153|ref|XP_862298.1|" > > > > protein_descr="gi|73975153|ref|XP_862298.1| PREDICTED: hypothetical > > > > protein XP_857205 isoform 4 [Canis familiaris]"/> > > > > <search_score name="pvalue" value="0.000002382663488"/> > > > > <search_score name="expect" value="0.028320338214958"/> > > > > </search_hit> > > > > > For decoy string, it looks like this: > > > > > <search_hit hit_rank="2" peptide="QESARYSAKVTVAGLEESATEAQQQIR" > > > > peptide_prev_aa="K" peptide_next_aa="S" protein="decoy_2098 > > > > 2" num_tot_proteins="1" num_matched_ions="17" tot_num_ions="52" > > > > calc_neutral_pep_mass="2949.481" massdiff="0.9728599071700 > > > > 05" is_rejected="0" protein_descr="decoy_20982"> > > > > <search_score name="pvalue" value="0.000014221885248"/> > > > > <search_score name="expect" value="0.168173793062284"/> > > > > </search_hit> > > > > > On Jul 2, 4:44 pm, Jimmy Eng <[email protected]> wrote: > > > >> Ping, > > > > >> I just downloadedOMSSA2.1.4 and tried the direct pep.xml export > > > >> myself. I do see a problem with the resulting pep.xml file that the > > > >> "-op" option generates that's causing the problem you're seeing. > > > > >> The key error message in your output is this: > > > >> WARNING: No decoys with label DECOY were found in this dataset. > > > > >> Looking at the generated pep.xml files,OMSSAseems to be placing some > > > >> number in the protein="" attribute of each search_hit element. Whereas > > > >> PeptideProphet expects this protein attribute to contain some protein > > > >> identifier that includes the DECOY string for those decoy matches. In > > > >> the converters we use, the value of the protein attribute is the first > > > >> word of the protein definition line. > > > > >> As for a fix, we need someone at NCBI to address this and hopefully > > > >> someone here will contact them about this. For you in the short term, > > > >> you're going to need a developer to modify you pep.xml files to replace > > > >> the value in the "protein" attribute with the first word from the > > > >> "protein_descr" attribute of each search_hit entry. > > > > >> - Jimmy > > > > >> Ping wrote: > > > >>> Hi, > > > >>> I am trying to run the xinteract on theomssapep.xml output files. my > > > >>>omssa'sversion is 2.1.4, my TPP version is 4.2.1. But I couldn't get > > > >>> it through. I search the old post, there is a similar post, but the > > > >>> problem was solved by specifying enzyme to xinteract. > > > >>> I tried it, but is still not working. InteractParse went through, but > > > >>> PeptideProphetParser got stuck by a segmentation fault. > > > >>> Any help would be greatly appreciated! > > > >>> Many Thanks, > > > >>> Ping > > > >>> ***** output for interactParser and PeptideProphetParser > > > >>> InteractParser 'interact.pep.xml' 'omssa.pep.xml' -L'7' -E'trypsin' -C > > > >>> -P > > > >>> file 1: ParoSaliv_SHAM_03.pep.xml > > > >>> processed altogether 2623 results > > > >>> PeptideProphetParser 'interact.pep.xml' DECOY=DECOY MINPROB=0 > > > >>> NONPARAM > > > >>> Using Decoy Label "DECOY". > > > >>> Using non-parametric distributions > > > >>> (OMSSA) (minprob 0) > > > >>> WARNING!! The discriminant function forOMSSAis not yet complete. It > > > >>> is presented here to help facilitate trial and discussion. Reliance > > > >>> on this code for publishable scientific results is not recommended. > > > >>> init withOMSSATrypsin > > > >>> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > > > >>> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > > >>> PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905131510 > > > >>> (linux)) akel...@isb > > > >>> read in 75 1+, 1790 2+, 749 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > > > >>> Initialising statistical models ... > > > >>> WARNING: No decoys with label DECOY were found in this dataset. > > > >>> reverting to fully unsupervised method. > > > >>> Iterations: .........10.........20 > > > >>> Segmentation fault --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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