Hi Honglan, I am on vacation this week. I did fix another processing issue with MSGF+ earlier, but I was still testing. I will get back to you once I'm back next week.
David On Apr 13, 2016 12:14 AM, "Honglan Li" <[email protected]> wrote: > 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. > 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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