Your best bet is to try the code from trunk SVN. Have you tried it in NONPARAM mdoe?
-David On Wed, Feb 2, 2011 at 12:52 PM, Andreas Quandt <[email protected]> wrote: > hey jimmy and matt, > i tried what jimmy suggested but are stuck again.... :-( > i added the 'missing' scores as jimmy suggested: > <search_score name="deltacn" value="0.22324939" /> > <search_score name="xcorr" value="0.96492940" /> > <search_score name="deltacnstar" value="0.000"/> > <search_score name="spscore" value="0.0000"/> > <search_score name="sprank" value="1"/> > and get following output: > running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser > 'interact.pep.xml' DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI > INSTRWARN" > using Accurate Mass Bins > using pI > Using no error on different instrument types. > Using Decoy Label "DECOY_". > Decoy Probabilities will be reported. > Using non-parametric distributions > (SEQUEST) (leaving deltacn* entries) > adding Accurate Mass mixture distr > adding pI mixture distr > init with SEQUEST trypsin > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.00210.00210.4. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.00234.00234.3. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.00668.00668.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.01888.01888.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.01912.01912.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.01913.01913.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.02423.02423.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.02440.02440.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.02441.02441.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.03150.03150.3. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.03171.03171.3. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.04499.04499.3. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.04599.04599.4. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.06133.06133.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.06134.06134.2. This spectrum will be excluded from the model. > ERROR: Discriminant value computed as nan, for spectrum > B08-02057.07676.07676.4. This spectrum will be excluded from the model. > MS Instrument info: Manufacturer: NA, Model: NA, Ionization: NA, Analyzer: > UNKNOWN, Detector: UNKNOWN > PeptideProphet (TPP v4.4 VUVUZELA rev 1, Build 201102011840 (linux)) > AKeller@ISB > read in 0 1+, 5 2+, 416 3+, 26 4+, 2 5+, 1 6+, and 0 7+ spectra. > Initialising statistical models ... > Found 238 Decoys, and 212 Non-Decoys > Iterations: .PeptideProphetParser: > Validation/InterProphet/InterProphetParser/KDModel.cxx:143: bool > KDModel::replaceProb(int, double): Assertion `idx < posprobs_->size()' > failed. > command "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser 'interact.pep.xml' > DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI INSTRWARN" exited with > non-zero exit code: 6 > QUIT - the job is incomplete > the errors are coursed by negative values for the xcorr. hence i 'turned' > them into positive values. however this only causes another error: > command completed in 1 sec > running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser > 'interact.pep.xml' DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI > INSTRWARN" > using Accurate Mass Bins > using pI > Using no error on different instrument types. > Using Decoy Label "DECOY_". > Decoy Probabilities will be reported. > Using non-parametric distributions > (SEQUEST) (leaving deltacn* entries) > adding Accurate Mass mixture distr > adding pI mixture distr > init with SEQUEST trypsin > command "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser 'interact.pep.xml' > DECOY=DECOY_ ACCMASS DECOYPROBS NONPARAM LEAVE PI INSTRWARN" exited with > non-zero exit code: 11 > QUIT - the job is incomplete > > as i do not know what these error codes mean, i am now stuck :-( > does one of you guys have a suggestion how to continue? > cheers, > andreas > On Wed, Feb 2, 2011 at 6:49 PM, Andreas Quandt <[email protected]> > wrote: >> >> Hey Jimmy, >> >> I tried the renaming but of course not the adding of the 'missing' >> scoring values. >> I report back to you guys as soon as I have tested it :-) >> >> Cheers, >> Andreas >> >> >> >> On Feb 2, 2011, at 5:51 PM, Jimmy Eng <[email protected]> wrote: >> >> > Andreas, >> > >> > I didn't say it was going to be easy! :) >> > >> > Here's an example Sequest pep.xml file: >> > http://proteomicsresource.washington.edu/dist/sequest.pep.xml >> > >> > As Matt suggested, the search_score names will need to change >> > ("xcorr_score" to "xcorr" and "delta_cn" to "deltacn"). Additionally, >> > you'll probably want to add "deltacnstar", "spscore", and "sprank" >> > score entries. Use 0.0, 0.0, and 1 respectively for the values for >> > these additional scores. >> > >> > - Jimmy >> > >> > On Wed, Feb 2, 2011 at 8:42 AM, Matthew Chambers >> > <[email protected]> wrote: >> >> Did you try renaming the score names? I expect that there is a 1:1 >> >> relationship between the search engine name and the score names >> >> (correct me >> >> if I'm wrong TPP folks). If you need a program to do the "replace all" >> >> you >> >> can try Notepad++ or Gvim. >> >> >> >> -Matt >> >> >> >> >> >> On 2/2/2011 10:22 AM, Andreas Quandt wrote: >> >>> >> >>> sure :-) >> >>> >> >>> originally the spectrum query match looks like >> >>> >> >>> <spectrum_query spectrum="B08-02057.mzXML.00234.00234.3" >> >>> >> >>> but after it did not work. i tried the B08-02057.00234.00234.3 >> >>> instead: >> >>> >> >>> >> >>> <spectrum_query spectrum="B08-02057.00234.00234.3" start_scan="234" >> >>> end_scan="234" >> >>> precursor_neutral_mass="1332.6912" assumed_charge="3" index="4"> >> >>> <search_result> >> >>> <search_hit hit_rank="2" peptide="GAFALTLIGLLLM" peptide_prev_aa="R" >> >>> peptide_next_aa="-" >> >>> protein="DECOY_Q8TE58" num_tot_proteins="1" >> >>> calc_neutral_pep_mass="1332.7074" massdiff="-0.0162" >> >>> num_tol_term="2" num_missed_cleavages="0" is_rejected="0" >> >>> protein_descr="\ID=ATS15_HUMAN \MODRES= >> >>> \VARIANT=(623|N|S)(770|Q|R)(878|C|G) \NCBITAXID=9606 \DE=A disintegrin >> >>> and >> >>> metalloproteinase with >> >>> thrombospondin motifs 15 (ADAMTS-15) (ADAM-TS 15) (ADAM-TS15)"> >> >>> <search_score name="delta_cn" value="0.00000000" /> >> >>> <search_score name="xcorr_score" value="-0.04533549" /> >> >>> </search_hit> >> >>> </search_result> >> >>> </spectrum_query> >> >>> <spectrum_query spectrum="B08-02057.00244.00244.5" start_scan="244" >> >>> end_scan="244" >> >>> precursor_neutral_mass="2591.2581" assumed_charge="5" index="5"> >> >>> <search_result> >> >>> <search_hit hit_rank="1" peptide="HMLDVLLLFIAVIVALPVLAELGM" >> >>> peptide_prev_aa="R" peptide_next_aa="-" >> >>> protein="DECOY_P10635" num_tot_proteins="1" >> >>> calc_neutral_pep_mass="2591.2922" massdiff="-0.0342" >> >>> num_tol_term="2" num_missed_cleavages="0" is_rejected="0" >> >>> protein_descr="\ID=CP2D6_HUMAN \MODRES= >> >>> >> >>> >> >>> \VARIANT=(11|V|M)(26|R|H)(28|R|C)(34|P|S)(42|G|R)(85|A|V)(91|L|M)(94|H|R)(107|T|I)(120|F|I)(155|E|K)(169|G|R)(212|G|E)(231|L|P)(237|A|S)(281|.|)(296|R|C)(297|I|"> >> >>> <search_score name="delta_cn" value="0.00000000" /> >> >>> <search_score name="xcorr_score" value="0.37809423" /> >> >>> </search_hit> >> >>> </search_result> >> >>> </spectrum_query> >> >>> <spectrum_query spectrum="B08-02057.00246.00246.4" start_scan="246" >> >>> end_scan="246" >> >>> precursor_neutral_mass="2007.0232" assumed_charge="4" index="6"> >> >>> <search_result> >> >>> >> >>> (to the original sequest, the difference is also that the scores are >> >>> named: xcorr and deltacn...) >> >>> >> >>> --andreas >> >>> >> >>> On Wed, Feb 2, 2011 at 5:04 PM, Matthew Chambers >> >>> <[email protected] >> >>> <mailto:[email protected]>> wrote: >> >>> >> >>> Can you paste a few of the spectrum_query elements? It seems like >> >>> you >> >>> got it to process properly >> >>> as SEQUEST, so there's something wrong further down. >> >>> >> >>> -Matt >> >> >> >> -- >> >> 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]. >> >> 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. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [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. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [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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