Hi David It's me again.
Thanks for giving me new PeptideProphet file to run MS_GF+ results. But it still has problem to execute new test file. Would you please tell me the reason? Thanks a lot. Honglan Li XML file: https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing Recieved msg: ---- KDModel.cpp, Line 144 Expression: idx < posprobs_ -> size() This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information ---- Thanks a lot. Honglan Li 2016년 3월 30일 수요일 오후 8시 30분 5초 UTC+9, Honglan Li 님의 말: > > > Hi David. > > It's me again. > > Last time, you gave me the s/w and cmd. > > It's works well when I use the sample I gave you, and some other XML files. > > But for some XML files, it still do not work well. > > XML file: > https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing > > > When I executed this test sample (test2.pep.xml.xml) with the cmd you told > me > > "PeptideProphetParser.exe test2.pep.xml.xml NONPARAM > DECOY=XXX DECOYPROBS MINPROB=0 CLEVEL=2 ACCMASS PPM" > > I received msg as follows: (detail: I added captured error msg file) > > ---- > KDModel.cpp, Line 144 > Expression: idx < posprobs_ -> size() > > This application has requested the Runtime to terminate it in an unusual > way. > Please contact the application's support team for more information > ---- > > Would you please tell me what happened to this XML file? > > Thanks a lot. > > Honglan Li > > > > 2016년 3월 28일 월요일 오전 8시 52분 13초 UTC+9, Honglan Li 님의 말: >> >> Thank you very much for your help, David. >> >> It works well now. >> >> Best wishes, >> Honglan Li >> >> >> 2016년 3월 26일 토요일 오전 2시 33분 59초 UTC+9, David Shteynberg 님의 말: >>> >>> Hello Honglan, >>> >>> I was unable to replicate the error on my system, however, I have tested >>> that this command works on a more recently compiled version of >>> PeptideProphet. You can download the binary here >>> https://dl.dropboxusercontent.com/u/21286225/PeptideProphetParser.exe >>> and run as follows >>> >>> PeptideProphetParser.exe test.pep.xml NONPARAM DECOY=XXX DECOYPROBS >>> MINPROB=0 CLEVEL=2 ACCMASS PPM >>> >>> >>> I had to set a fairly high CLEVEL value on this data since MSGF+ suffers >>> from scoring highly of some decoys and is not always accurate at the >>> critical 1% error. The WARNING message in the new code has been updated to >>> reflect this problem. >>> >>> Cheers, >>> -David >>> >>> >>> On Thu, Mar 24, 2016 at 8:21 PM, Honglan Li <[email protected]> wrote: >>> >>>> Thanks for your quick reply. >>>>> >>>> >>>> I tried the command you told me, but it stll didn't work well. >>>> >>>> The warning msg is "*The discriminant function for MSGFPL is not >>>> yet complete" * >>>> >>>> How to fix it ? >>>> >>>> >>>> *cmd*: >>>> >>>> xinteract -OPd -p0 -dXXX_ *.xml >>>> >>>> >>>> >>>> *Error msg I received* >>>> >>>> ---- >>>> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'" >>>> command completed in 0 sec >>>> >>>> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' >>>> 'C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>> CYH\uniprot_C+H+Y+48.revCat.fasta'" >>>> - Building Commentz-Walter keyword tree... - Searching the >>>> tree...opening "C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>> CYH\uniprot_C+H+Y+48.revCat.fasta" as >>>> "/home/mllab/hllee/uniprot_C+H+Y+48.revCat.fasta" >>>> >>>> - Linking duplicate entries... - Printing results... >>>> >>>> command completed in 11 sec >>>> >>>> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' >>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" >>>> Using Decoy Label "XXX_". >>>> Decoy Probabilities will be reported. >>>> Using non-parametric distributions >>>> (MS-GF+) (minprob 0) >>>> WARNING!! *The discriminant function for MSGFPL is 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 with MS-GF+ trypsin >>>> Segmentation fault (core dumped) >>>> >>>> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' >>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" exited with non-zero exit code: >>>> 35584 >>>> QUIT - the job is incomplete >>>> >>>> ----- >>>> >>>> *XML format per PSM: (file: * >>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3Y2diWDAzVHBQSm8/view?usp=sharing >>>> ) >>>> >>>> <spectrum_query >>>> spectrum="C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1. >>>> CYH\C-25fmol-R1_QEx2_000090.51174.51174.4" spectrumNativeID="index=51174" >>>> start_scan="51174" end_scan="51174" >>>> precursor_neutral_mass="3972.990669523105" assumed_charge="4" index="1"> >>>> <search_result> >>>> <search_hit hit_rank="1" >>>> peptide="VGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPR" peptide_prev_aa="R" >>>> peptide_next_aa="F" protein="sp|P16521|EF3A_YEAST" num_tot_proteins="1" >>>> calc_neutral_pep_mass="3972.99140194498" massdiff="7.32421875e-04" >>>> protein_descr="sp|P16521|EF3A_YEAST Elongation factor 3A OS=Saccharomyces >>>> cerevisiae (strain ATCC 204508 / S288c) GN=YEF3 PE=1 SV=4" >>>> num_tol_term="2" >>>> num_missed_cleavages="1"> >>>> <search_score name="raw" value="269"/> >>>> <search_score name="denovo" value="289"/> >>>> <search_score name="SpecEValue" >>>> value="2.8337685502588284E-39"/> >>>> <search_score name="EValue" value="1.2856572993111488E-31"/> >>>> <search_score name="IsotopeError" value="0"/> >>>> </search_hit> >>>> </search_result> >>>> </spectrum_query> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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 post to this group, send email to [email protected]. >>>> 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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