Luis, Thanks for your message. I rerun the experiment leaving all options same except -he option [-he evalcut command line option to omssacl] for OMSSA seach set to 1,000,000 then
I got total hits of 309 while running ProphetModels.pl corresponding to 575 decoys and 1478 non-decoys. Here is the brief program output .... ---------------------------------------------------------------------------------------------------------- read in 187 1+, 885 2+, 981 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 575 Decoys, and 1478 Non-Decoys -------------------------------------------------------------------------------------------------------------- Here is the output from the corresponding previous run with -he=1 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 ---------------------------------------------------------------------------------------------------- In the current case study I have used the following commandline options while running OMSSA search .... --------------------------------------------------------------------------------------------------------------------------------------------------------------- /home/APCF/omssa-2.1.7.linux/omssacl -cl 0 -d /mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta -e 0 -fm /home/APCF/omssa/spectra/0f3ad159ab3ed187e2d43fe8d6134dac_3.mgf -he 1000000 -hl 10 -ht 6 -i 1,4 -mm 128 -mux /home/APCF/omssa-2.1.7.linux/usermods.xml -mx /home/APCF/omssa-2.1.7.linux/mods.xml -ox /home/APCF/omssa/results/0f3ad159ab3ed187e2d43fe8d6134dac/0f3ad159ab3ed187e2d43fe8d6134dac_3.omx -pc 1 -sct 0 -sp 100 -te 2 -tem 0 -to 0.8 -tom 0 -v 1 -w -x 0 -z1 0.95 -zh 3 -zl 1 -zt 3 --------------------------------------------------------------------------------------------------------------------------------------------------------------- After OMSSA search, I use omssa2pepXML command from omssa distribution (omssa-2.1.7.linux) to generate pepXML file. When I run ProphetModels.pl after InterProphetParser merger then I see the following .... ----------------------------------------------------------- Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-09-08/jagan-J1557 (MASCOT)"... => Total of 119 hits. Parsing search results "jagan-J1558 (X! Tandem (k-score))"... => Total of 239 hits. Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-09-08/jagan-J1561 (OMSSA)"... => Total of 152 hits. ---------------------------------------------------------------- here are the similar entries corresponding to previous run where the OMSSA command line option used for -he was 1 ---------------------------------------------------------------------------------------------------------------------------------- Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-09-03/jagan-J1366 (MASCOT)"... => Total of 124 hits. Parsing search results "jagan-J1367 (X! Tandem (k-score))"... => Total of 335 hits. Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-09-03/jagan-J1370 (OMSSA)"... => Total of 0 hits. ------------------------------------------------------------- The results are so much different could you mind to advise which is the better value for OMSSA command line option -he to choose. with regards, Jagan Kommineni On Tue, Sep 7, 2010 at 11:16 AM, Luis Mendoza <[email protected]>wrote: > 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. > 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. > -- 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.
