Hello Jagan, Based on the output you provided, it seems that you are not giving PeptideProphet that many search results to begin with:
read in 0 1+, 99 2+, 31 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Which corresponds to the 130 reported results. How did you search your data through OMSSA? How was the input file jagan-J1370.pep.xml generated? How many results do you see when you open this file in PepXMLViewer, especially compared to the Mascot and Tandem pep.xml results? Ultimately, the model fails due to the very low number of search hits in the input file. We will look into providing a better error message when this is encountered, since "exit code: 11" is not too useful! --Luis On Mon, Sep 6, 2010 at 5:55 PM, Jagan Kommineni <[email protected]>wrote: > > > On Fri, Sep 3, 2010 at 2:51 PM, Jagan Kommineni <[email protected] > > wrote: > >> Dear All, >> >> I have taken RAW file generated by Instrument info: Manufacturer: Thermo >> Finnigan, Model: LCQ Deca, Ionization: nanoelectrospray, Analyzer: >> quadrupole ion trap, Detector: electron multiplier and run standard search >> using Mascot, X!tandem and OMSSA and fed the data through TPP pipeline then >> I found that 0 (zero) decoy and 130 non-decoy entries for the search >> results of OMSSA whereas 545 Decoys and 785 Non-Decoys entries for Mascot >> search results and 536 Decoys and 833 Non-Decoys entries for x!tandem >> search. >> >> I found total hits retruned from Mascot and X!tandem search result sets >> respectively are of 303 and 351. >> >> >> For OMSSA based search results, the PeptideProphetParser program quitted >> with exit code of 11. >> >> Here is the complete STDOUT of OMSSA and TPP pipeleine ... >> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> /home/APCF/tpp/bin/xinteract -Njagan-J1370.pepprophet.xml -eT -d'sp|decoy' >> -p0.05 -l7 -x20 -R -OP jagan-J1370.pep.xml >> >> /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development >> prerelease) rev 0, Build 201007011135 (linux)) >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >> 'jagan-J1370.pepprophet.xml' 'jagan-J1370.pep.xml' -P -L'7' -E'trypsin'" >> file 1: jagan-J1370.pep.xml >> processed altogether 130 results >> >> >> results written to file >> /mnt/sanfs/APCF/results/tpp/2010-09-03/jagan-J1370.pepprophet.shtml >> >> >> >> command completed in 0 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1370.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> NONPARAM" >> Using Decoy Label "sp|decoy". >> Using non-parametric distributions >> (OMSSA) >> WARNING!! The discriminant function for OMSSA 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 OMSSA trypsin >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> >> PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev >> 0, Build 201007011135 (linux)) akel...@isb >> read in 0 1+, 99 2+, 31 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Found 0 Decoys, and 130 Non-Decoys >> WARNING: No decoys with label sp|decoy were found in this dataset. >> reverting to fully unsupervised method. >> Iterations: .........10.........20 >> >> command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1370.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> NONPARAM" exited with non-zero exit code: 11 >> QUIT - the job is incomplete >> >> ============================================================================================== >> >> I wonder is there any requirement to have at least few decoy entries for >> PeptideProphetParser to continue without fail? >> >> Further study with pep XML generated by different algorithm search >> results, I found that there is only one decoy entry for xml tag of >> search_hit which I am here with enclosing in this mail ... >> >> ------------------------------------------------------------ >> <search_hit hit_rank="2" peptide="LGDSEVDIGIMANLDIVESKR" >> peptide_prev_aa="K" peptide_next_aa="L" protein="520685" >> num_tot_proteins="2" num_matched_ions="21" tot_num_ions="40" >> calc_neutral_pep_mass="2273.156" massdiff="0.041999999999865" >> is_rejected="0" protein_descr="sp|decoy_C1ERL6|ACDH_BACC3 Reverse sequence, >> was Acetaldehyde dehydrogenase OS=Bacillus cereus (strain 03BB102) >> GN=BCA_2154 PE=3 SV=1"> >> <alternative_protein protein="520683" >> protein_descr="sp|decoy_A0RD69|ACDH_BACAH Reverse sequence, was Acetaldehyde >> dehydrogenase OS=Bacillus thuringiensis (strain Al Hakam) GN=BALH_1843 PE=3 >> SV=1"/> >> <search_score name="pvalue" value="0.000012588862528"/> >> <search_score name="expect" value="0.648238298133515"/> >> </search_hit> >> ----------------------------------------------------------- >> >> whereas I found 581 and 572 similar tags in Mascot and X!tandem based >> results, >> >> with regards, >> >> -- >> Dr. Jagan Kommineni >> Ludwig Institute for Cancer research >> Pakville VIC 3145 >> Australia. >> >> > > > -- > Dr. Jagan Kommineni > Ludwig Institute for Cancer research > Pakville VIC 3145 > Australia. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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