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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