Don't forget the -P option in the first command for OMSSA. InteractParser 'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' -E'trypsin'" -P
On Tue, Jul 20, 2010 at 11:53 PM, David Shteynberg <[email protected]> wrote: > Dear Jagan, > > You must run the steps of xinteract separately for this option in > version 4.3.1. The -P option is specified at the InteractParser step. > The sequence should be: > > InteractParser 'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' > -E'trypsin'" > RefreshParser 'davidtest.pepprophet.xml' `DatabaseParser > davidtest.pepprophet.xml` > PeptideProphetParser 'davidtest.pepprophet.xml' NONPARAM DECOYPROBS > DECOY=DECOY > > *notice the backticks in the second command > > -David > > > > On Tue, Jul 20, 2010 at 11:38 PM, Jagan Kommineni > <[email protected]> wrote: >> Deall All, >> >> I am trying to pass -P options from the xinteract by specifying -P (fix >> protein names in OMSSA data) but couldn't get it work. Here is the STDOUT >> for OMSSA-TPP pipeline with xinteract which has some issues in writing >> output file for InteractParser which lead to failure of the pipeline but >> when I run InteractParser with -P options and leaving all the other options >> remin same then the OMSSA-TPP pipeline completes. >> >> -------------------------------------------------------------------------------------------------------------------------- >> [r...@apcf-hn3 DavidTest]# /home/APCF/tpp/bin/xinteract -P >> -Ndavidtest.pepprophet.xml -OPd -dDECOY -eT davidtest.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 >> 'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' -E'trypsin'" >> file 1: davidtest.pep.xml >> processed altogether 2445 results >> >> >> results written to file >> /mnt/sanfs/APCF/results/tpp/2010-07-19/DavidTest/davidtest.pepprophet.shtml >> >> >> >> command completed in 7 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY" >> Using Decoy Label "DECOY". >> Decoy Probabilities will be reported. >> 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 417 1+, 1290 2+, 361 3+, 54 4+, 3 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Found 0 Decoys, and 2125 Non-Decoys >> WARNING: No decoys with label DECOY were found in this dataset. reverting to >> fully unsupervised method. >> Iterations: .........10.........20 >> >> command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY" exited with >> non-zero exit code: 11 >> QUIT - the job is incomplete >> [r...@apcf-hn3 DavidTest]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >> 'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' -E'trypsin' -P >> file 1: davidtest.pep.xml >> processed altogether 2445 results >> >> >> results written to file >> /mnt/sanfs/APCF/results/tpp/2010-07-19/DavidTest/davidtest.pepprophet.shtml >> >> >> >> [r...@apcf-hn3 DavidTest]# >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY >> Using Decoy Label "DECOY". >> Decoy Probabilities will be reported. >> 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 417 1+, 1290 2+, 361 3+, 54 4+, 3 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Found 903 Decoys, and 1222 Non-Decoys >> Iterations: .........10.........20...... >> WARNING: Mixture model quality test failed for charge (1+). >> WARNING: Mixture model quality test failed for charge (5+). >> WARNING: Mixture model quality test failed for charge (6+). >> WARNING: Mixture model quality test failed for charge (7+). >> model complete after 27 iterations >> [r...@apcf-hn3 DavidTest]# >> --------------------------------------------------------------------------------- >> >> I notice the following difference when I run InteractParser with and without >> "-P" option. >> >> ------------------------------------------------------- >> WITHOUT "-P" OPTION >> ---------------------------------- >> < <search_hit hit_rank="2" peptide="VTSGTALLFVVTD" peptide_prev_aa="R" >> peptide_next_aa="M" protein="24347" num_tot_proteins="1" >> num_matched_ions="5" tot_num_ions="24" calc_neutral_pep_mass="1321.712" >> massdiff="-0.750000000000011" is_rejected="0" protein_descr="DECOY_Q5VST9 >> Decoy sequence" num_tol_term="1" num_missed_cleavages="0"> >> --- >> WITH "-P" OPTION >> ---------------------------- >>> <search_hit hit_rank="2" peptide="VTSGTALLFVVTD" peptide_prev_aa="R" >>> peptide_next_aa="M" protein="DECOY_Q5VST9" num_tot_proteins="1" >>> num_matched_ions="5" tot_num_ions="24" calc_neutral_pep_mass="1321.712" >>> massdiff="-0.750000000000011" is_rejected="0" protein_descr="DECOY_Q5VST9 >>> Decoy sequence" num_tol_term="1" num_missed_cleavages="0"> >> ------------------------------------------------------- >> WITHOUT "-P" OPTION >> ---------------------------------- >> < <search_hit hit_rank="3" peptide="MITVVYGPDLVN" peptide_prev_aa="R" >> peptide_next_aa="I" protein="26762" num_tot_proteins="1" >> num_matched_ions="5" tot_num_ions="22" calc_neutral_pep_mass="1319.678" >> massdiff="1.283999999999989" is_rejected="0" protein_descr="Q9NQ66 >> PLCB1_HUMAN 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-1 >> OS=Homo sapiens GN=PLCB1 PE=1 SV=1" num_tol_term="1" >> num_missed_cleavages="0"> >> ------------------------------------------------------- >> WITH "-P" OPTION >> ---------------------------------- >>> <search_hit hit_rank="3" peptide="MITVVYGPDLVN" peptide_prev_aa="R" >>> peptide_next_aa="I" protein="Q9NQ66" num_tot_proteins="1" >>> num_matched_ions="5" tot_num_ions="22" calc_neutral_pep_mass="1319.678" >>> massdiff="1.283999999999989" is_rejected="0" protein_descr="Q9NQ66 >>> PLCB1_HUMAN 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-1 >>> OS=Homo sapiens GN=PLCB1 PE=1 SV=1" num_tol_term="1" >>> num_missed_cleavages="0"> >> ------------------------------------------------ >> >> Any suggestions please. >> >> >> with regards, >> >> >> 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]. >> 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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