If you're running this using xinteract, you can debug a little by adding "-t!" to the xinteract commandline on the release version, and "-t#" to the commandline for the development version. "-t!" (note the exclamation point) causes a series of test files to be generated (they're just copies of the output as the job progresses) and "-t#" causes the software to check its progress against those files. This may help you figure out where things are going wrong.
On Wed, Jun 23, 2010 at 12:28 AM, Jagan Kommineni <[email protected] > wrote: > Dear All, > > When I run the TPP pipeline with downloaded version of the > development prerelease of TPP dated 22-04-2010, I am getting 0 hits > whereas when I run pipeline with release version of TPP (TPP v4.3 > (jetstream) rev 1) for the same data and parameters, I am getting 822 > hits. > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------ > Here is the STDOUT when I run the TPP pipeline with > development version downloaded on 22-04-2010 > > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- > /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development > prerelease) rev 0, Build 201006041141 (linux)) > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan- > J78.pepprophet.xml' 'jagan-J78.pep.xml' -L'7'" > > file 1: jagan-J78.pep.xml > > processed altogether 3429 results > > results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan- > J78.pepprophet.shtml > > command completed in 1 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'jagan- > J78.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20" > > (X! Tandem (k-score)) > > init with X! Tandem (k-score) trypsin > > MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ > Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: > inductive detector > > Initialising statistical models ... > > Iterations: .........10.........20........ > > model complete after 29 iterations > > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i jagan- > J78.pepprophet.xml" > > Analyzing jagan-J78.pepprophet.xml ... > > Parsing search results "jagan-J77 (X! Tandem (k-score))"... > > => Total of 0 hits. > > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan- > J78.pepprophet.xml'" > > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan- > J78.pepprophet.xml' '/home/APCF/databases/SwissProt/ > uniprot_sprot.fasta'" > > - Searching the tree... > > - Linking duplicate entries... - Printing results... > > command completed in 3 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I / > mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" > > command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /mnt/ > sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" exited > with non-zero exit code: 11 > > QUIT - the job is incomplete > > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.4 JETSTREAM (unstable development > prerelease) rev 0, Build 201006041141 (linux)) > > (xml input) (report Protein Length) (using degen pep info) > > . . . reading in /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan- > J78.pepprophet.xml. . . > > did not find any PeptideProphet results in input data! Did you forget > to run PeptideProphet? > > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with > min prob 0.05 > > no data - quitting > > ============================================================================== > But when I run the same thing with release version of TPP (TPP v4.3 > (jetstream) rev 1) everything went OK. > Here is the STDOUT message .... > > --------------------------------------------------------------------------------------------------------------------------------------------------------------- > > [r...@compute-3-0 temp]# pwd > /mnt/sanfs/APCF/results/tpp/2010-06-23/temp > [r...@compute-3-0 temp]# ls > jagan-J77.mzXML jagan-J77.xml > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/Tandem2XML jagan-J77.xml jagan-J78.pep.xml > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/InteractParser jagan-J78.pepprophet.xml jagan-J78.pep.xml - > L7 > file 1: jagan-J78.pep.xml > processed altogether 3429 results > > results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/temp/ > jagan-J78.pepprophet.shtml > > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/PeptideProphetParser jagan-J78.pepprophet.xml MINPROB=0.05 > EXTRAITRS=20 > (X! Tandem (k-score)) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ > Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: > inductive detector > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 201003241044 > (linux)) akel...@isb > read in 1127 1+, 1355 2+, 361 3+, 54 4+, 0 5+, 0 6+, and 0 7+ > spectra. > Initialising statistical models ... > negmean = -0.490485 > negmean = -0.0225753 > negmean = -0.520051 > negmean = 0.801738 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > Iterations: .........10.........20........ > WARNING: Mixture model quality test failed for charge (1+). > model complete after 29 iterations > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/ProphetModels.pl -i jagan-J78.pepprophet.xml > Analyzing jagan-J78.pepprophet.xml ... > Parsing search results "jagan-J77 (X! Tandem (k-score))"... > => Total of 822 hits. > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/DatabaseParser jagan-J78.pepprophet.xml > /home/APCF/databases/SwissProt/uniprot_sprot.fasta > [r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/ > build/linux/RefreshParser jagan-J78.pepprophet.xml /home/APCF/ > databases/SwissProt/uniprot_sprot.fasta > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > [r...@compute-3-0 temp]# > > ============================================================================== > > I wonder whether there is any quick fix to this problem. Something > broken from the release version to development version. > > with regards, > > Jagan Kommineni > > > > > -- > 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]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
