[spctools-discuss] Maldi data protein prophet problem
hi everyone, There is a problem with my protein prophet. It cannot display the results and shows the following error. c:/Inetpub/wwwroot/ISB/data/probidoutput/swissprot/interact.prot.shtml [ Unreadable! ] If I choose the pre-generate static html file for loading to browser option when running protein prophet, the same situation still happens, but a readable html is generated. The html generated seems to be functioning well and normal. * c:/Inetpub/wwwroot/ISB/data/probidoutput/swissprot/ interact.prot.shtml [ Unreadable! ] * c:/Inetpub/wwwroot/ISB/data/probidoutput/swissprot/ interact.prot.html [ View ] The more important problems is, when I choose the maldi data option in the peptide prophet, and click on the pre-generate static html file for loading to browser. The same dialog is displayed. * c:/Inetpub/wwwroot/ISB/data/probidoutput/swissprot/ interact.prot.shtml [ Unreadable! ] * c:/Inetpub/wwwroot/ISB/data/probidoutput/swissprot/ interact.prot.html [ View ] But this time, when I click on the interact.prot.html, there is only a white background and the following dailog is displayed. cannot find xml file c:/Inetpub/wwwroot/ISB/data/probidoutput/ swissprot/interact.prot.xml The search data is generated using probID. I run the same TPP procedure with 3 different computers and the same thing still happened. What can I do to solve the problem?? Thanks, Yan --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Unknown error during iterations in PeptideProphetParser
Dear all, I have TPP v4.3 installed on WindowsXP. I do not install cygwin and run the following lines in the MS DOS command or through the TPP GUI. Unknown error occurs during iterations in PeptideProphetParser. Can you have me some advice on this? Thank you very much in advance! Best regards, Melody Lam I run the following command at the directory C:\Inetpub\wwwroot\ISB \data\swissprot c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -OAm c:/ Inetpub/wwwroot/ISB/data/swissprot/analysis100.xml c:/Inetpub/wwwroot/ ISB/data/swissprot/analysis125.xml c:/Inetpub/wwwroot/ISB/data/ swissprot/analysis150.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis200.xml c:/Inetpub/wwwroot/ISB/data/swissprot/analysis25.xml c:/Inetpub/wwwroot/ISB/data/swissprot/analysis460.xml c:/Inetpub/ wwwroot/ISB/data/swissprot/analysis50.xml c:/Inetpub/wwwroot/ISB/data/ swissprot/analysis500.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis75.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysisunbind.xml Totally 10 xml files from OUT2XML are added. -- Here are the outputs: c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) running: C:/Inetpub/tpp-bin/InteractParser C:/Inetpub/wwwroot/tmp/ a02932/ISB/data/swissprot/interact.pep.xml c:/Inetpub/wwwroot/ISB/ data/swissprot/analysis100.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis125.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis150.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis200.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis25.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis460.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis50.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis500.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis75.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysisunbind.xml -L7 file 1: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis100.xml file 2: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis125.xml file 3: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis150.xml file 4: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis200.xml file 5: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis25.xml file 6: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis460.xml file 7: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis50.xml file 8: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis500.xml file 9: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis75.xml file 10: c:/Inetpub/wwwroot/ISB/data/swissprot/analysisunbind.xml processed altogether 9098 results results written to file c:/Inetpub/wwwroot/tmp/a02932/ISB/data/ swissprot/interact.pep.xml direct your browser to http://localhost/interact.pep.shtml command completed in 6 sec running: C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI using Accurate Mass Bins maldi mode (PROBID) adding Accurate Mass mixture distr init with PROBID Trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) AKeller@ ISB read in 8872 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .10.20 The Error dialog box pop up at this point during the iterations!!! I clicked Don't send on the box which ask if I should send any error report to Microsoft The following appears after clicking Don't Send command C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI failed: Unknown error command C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI exited with non -zero exit code: -1073741819 QUIT - the job is incomplete --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Unknown error during iterations in PeptideProphetParser
Hello Melody, It appears you've discovered a bug in the code with this particular analysis. Would you please zip up the data directory (or just the analysis*.xml files) and post them to our ftp site, instructions here: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F , so I can take a look and debug the problem? Thanks, -David On Wed, Sep 16, 2009 at 2:07 AM, Melody Lam paladinof...@gmail.com wrote: Dear all, I have TPP v4.3 installed on WindowsXP. I do not install cygwin and run the following lines in the MS DOS command or through the TPP GUI. Unknown error occurs during iterations in PeptideProphetParser. Can you have me some advice on this? Thank you very much in advance! Best regards, Melody Lam I run the following command at the directory C:\Inetpub\wwwroot\ISB \data\swissprot c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -OAm c:/ Inetpub/wwwroot/ISB/data/swissprot/analysis100.xml c:/Inetpub/wwwroot/ ISB/data/swissprot/analysis125.xml c:/Inetpub/wwwroot/ISB/data/ swissprot/analysis150.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis200.xml c:/Inetpub/wwwroot/ISB/data/swissprot/analysis25.xml c:/Inetpub/wwwroot/ISB/data/swissprot/analysis460.xml c:/Inetpub/ wwwroot/ISB/data/swissprot/analysis50.xml c:/Inetpub/wwwroot/ISB/data/ swissprot/analysis500.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis75.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysisunbind.xml Totally 10 xml files from OUT2XML are added. -- Here are the outputs: c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) running: C:/Inetpub/tpp-bin/InteractParser C:/Inetpub/wwwroot/tmp/ a02932/ISB/data/swissprot/interact.pep.xml c:/Inetpub/wwwroot/ISB/ data/swissprot/analysis100.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis125.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis150.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis200.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis25.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis460.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis50.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis500.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysis75.xml c:/Inetpub/wwwroot/ISB/data/swissprot/ analysisunbind.xml -L7 file 1: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis100.xml file 2: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis125.xml file 3: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis150.xml file 4: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis200.xml file 5: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis25.xml file 6: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis460.xml file 7: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis50.xml file 8: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis500.xml file 9: c:/Inetpub/wwwroot/ISB/data/swissprot/analysis75.xml file 10: c:/Inetpub/wwwroot/ISB/data/swissprot/analysisunbind.xml processed altogether 9098 results results written to file c:/Inetpub/wwwroot/tmp/a02932/ISB/data/ swissprot/interact.pep.xml direct your browser to http://localhost/interact.pep.shtml command completed in 6 sec running: C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI using Accurate Mass Bins maldi mode (PROBID) adding Accurate Mass mixture distr init with PROBID Trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) AKeller@ ISB read in 8872 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .10.20 The Error dialog box pop up at this point during the iterations!!! I clicked Don't send on the box which ask if I should send any error report to Microsoft The following appears after clicking Don't Send command C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI failed: Unknown error command C:/Inetpub/tpp-bin/PeptideProphetParser C:/Inetpub/wwwroot/ tmp/a02932/ ISB/data/swissprot/interact.pep.xml MINPROB=0.05 ACCMASS MALDI exited with non -zero exit code: -1073741819 QUIT - the job is incomplete --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at
[spctools-discuss] Re: intermediate folder of out and dta files
If you run the Sequest search through the TPP GUI interface or via the runsearch.exe wrapper on the command line, it would pack up and compress the search results folder and delete the corresponding directory (of dta/outs). You obviously don't need to keep the folders around if you have no use for those files. My suggestion would be to compress the .out files into a zip or tgz archive and then delete each directory only because the searches are expensive and there is esoteric bits of info in those files that aren't replicated in a pep.xml. If you do archive those files in a .tgz in a specific way, the link to the out files in the PepXML Viewer can still display the search results pulling the info directly from the compressed archive. You don't need to include the .dta files in the compressed archive because those spectra are easily recreated from the mzXML and the spectral display tool will grab corresponding spectrum from the mzXML file if present. On Wed, Sep 16, 2009 at 1:32 PM, Kris ktrunc...@gmail.com wrote: Anyone know what I need the intermediate folders for? -Kris On Sep 10, 4:49 pm, Kris ktrunc...@gmail.com wrote: Hi, I'm running a lot of database searches on a large number of mzXML files. Because of this, I need to conserve space on my computer. My understanding of the software is that Database Search generates afolderof out/dta files, which is converted to a PepXML file. The PepXML file is then used in Analyze Peptides to generate probability scores for matches. My question is: Is there any reason why I would want to save the folders of out/dta files? It seems like the only thing these folders are used for is generating PepXML files, and having the PepXML files is all I need. I would like to delete the folders of out/dtas to save space on my computer. But if there is some reason I should save them (something they could be used for later on), please let me know. Also, I noticed that if you run a large number of mzXML files in Database search, the search usually freezes after it gets to about 2.5 million lines of output (I believe). So, I've been running the commands in command line. Please let me know, if you see any problem with this. Thanks, Kris --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] about x!tandem PTM input
Dear friends, If I want to use the following PTM: Monoisotopic: -18.010565 Site:N Position: Protein C-term How should I set the input.xml parameters? 1. note type=input label=refine, potential C-terminus modifications-18.010...@n/note or 2.note type=input label=refine, potential C-terminus modifications-18.010...@]/note or 3.note type=input label=refine, potential modification mass-18.010...@n/note or 4.note type=input label=refine, potential modification mass-18.010...@]/note --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: about x!tandem PTM input
#2. see http://www.thegpm.org/TANDEM/api/refpctm.html I hate to state the obvious but this will only be applied in refinement mode so make sure that's turned on. On Wed, Sep 16, 2009 at 2:44 PM, rhodea rho...@gmail.com wrote: Dear friends, If I want to use the following PTM: Monoisotopic: -18.010565 Site: N Position: Protein C-term How should I set the input.xml parameters? 1. note type=input label=refine, potential C-terminus modifications-18.010...@n/note or 2.note type=input label=refine, potential C-terminus modifications-18.010...@]/note or 3.note type=input label=refine, potential modification mass-18.010...@n/note or 4.note type=input label=refine, potential modification mass-18.010...@]/note --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
