> > 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.
