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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
