Dear All, I have created decoy database for the SwisPlot database using decoyFASTA of the TPPDistribution and run the following TPP commands after the omssa search with decoy database and here is the output on STDOUT ...
--------------------------------------- [r...@compute-3-0 run-on-compute]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan-J128.pepprophet.xml' 'jagan-J128.pep.xml' -D'/home/APCF/databases/SwissProt/uniprot_sprot_Jan2009/decoy/decoy_uniprot_sprot.fasta' -L'7' -E'trypsin' -C -P file 1: jagan-J128.pep.xml processed altogether 126 results results written to file /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.pepprophet.shtml [r...@compute-3-0 run-on-compute]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'jagan-J128.pepprophet.xml' DECOY=decoy MINPROB=0 NONPARAM Using Decoy Label "decoy". Using non-parametric distributions (OMSSA) (minprob 0) 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 v4.3 JETSTREAM rev 1, Build 201003241044 (linux)) akel...@isb read in 0 1+, 82 2+, 44 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20..... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (4+). 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 26 iterations [r...@compute-3-0 run-on-compute]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan-J128.pepprophet.xml' '/home/APCF/databases/SwissProt/uniprot_sprot_Jan2009/decoy/decoy_uniprot_sprot.fasta' - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... [r...@compute-3-0 run-on-compute]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProteinProphet 'jagan-J128.pepprophet.xml' 'jagan-J128.prot.xml' ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 201003241044 (linux)) (xml input) (report Protein Length) (using degen pep info) . . . reading in /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.pepprophet.xml. . . . . . read in 0 1+, 0 2+, 33 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Could not find/open font when opening font "arial", using internal non-scalable font INFO: mu=6.3014e-09, db_size=584667857 protein probabilities written to file /mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.prot.xml direct your browser to http://nfs//mnt/sanfs/APCF/results/omssa/decoy_test_run/run-on-compute/jagan-J128.prot.shtml [r...@compute-3-0 run-on-compute]# ------------------------------------- I noticed there are some warning messages indicating some tests are failed, how critical are these messages. 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.
