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.
