My params file was named PAe000144_414_sequest.params. I will try your fix, and let you know if it works.
-Kris On Feb 20, 11:34 am, Jimmy Eng <[email protected]> wrote: > Kris, > > Is your search parameters file named "sequest.params" or > "PAe000144_414_sequest.params"? > > If it's not "sequest.params", this would explain the behavior. You're > able to specify a different name for the parameters file to run a search > but the downstream tools (i.e. Out2XML) aren't that flexible and > requires the parameter file to be named "sequest.params". If this is > the case, rename your file to sequest.params and try again (hopefully > you won't have to actually re-run the searches). > > Minimally we should make a quick mod to the TPP GUI to prevent allowing > a user from selecting a parameters file that's not named "sequest.params". > > - Jimmy > > Kris wrote: > > Hi Natalie, > > > I'm using mzxml files that I got from fromwww.peptideatlas.org/repository. > > The one I just ran was PAe000144, using the PAe000144_414_sequest > > params file. > > > I ran a database search on the last 6 mzxml files. The output files > > says they are Unreadable. The end of the output lines says that it's > > skipping 243489 lines of output, so it is getting output.My main > > concern is that at the end of the output lines, it says: > > "SequestParams: error opening 043005_900c/sequest.params > > > command "C:\Inetpub\tpp-bin\Out2XML.exe 043005_900c 1" failed: > > Operation not permitted > > > Command Successful". > > > It says at the top that I ran this command: > > run_in d:/Inetpub/wwwroot/ISB/data/PAe000144_mzXML_200709080112; > > runsearch -pd:/Inetpub/wwwroot/ISB/data/PAe000144_mzXML_200709080112/ > > PAe000144_414_sequest.params -P15 043005_060a.mzXML > > > This is wrong because I know I ran this command on all these mzxml > > files. The commands did not load back correctly after updating the > > page. > > Here is exactly what tthe output files say: > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_060a.pep.xml [ Unreadable! ] > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_060b.pep.xml [ Unreadable! ] > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_060c.pep.xml [ Unreadable! ] > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_900a.pep.xml [ Unreadable! ] > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_900b.pep.xml [ Unreadable! ] > > * d:/Inetpub/wwwroot/ISB/data/ > > PAe000144_mzXML_200709080112/043005_900c.pep.xml [ Unreadable! ] > > > And the last line of the output say: > > ...skipping 243489 lines of output... > > > 8. 8 / 8 0 2827.07162 0.2661 0.6742 66.6 9/92 > > YGL090W_id3058 K.ISNQSVIKMEDDDFDDFQFFGLSK.R > > 9. 9 / 55 0 2826.19648 0.2720 0.6688 40.7 7/96 > > YKR079C_id1787 R.FDTPLSRGTSMCKSQEEPLNTIIEK.D > > 10. 10 / 3 0 2827.09756 0.2832 0.6585 91.5 10/96 > > YLR127C_id4117 K.ALLSLVDTLHDSDINQDTNITKRDK.N > > > 38. 38 / 1 0 2826.15561 0.4631 0.4932 99.1 10/88 > > YBR136W_id340 K.KEDVRQDNQYMQFATTM#DFLLSK.D > > > 1. 0 YOL138C_id5498 > > 2. 0 YJR130C_id3891 > > 3. 0 YKL105C_id1588 > > > Total search time: 11 secs for 32 files > > Average search time: 0.34 secs > > > Out2XML 043005_900c 1 > > params file here: 043005_900c/sequest.params > > SequestParams: error opening 043005_900c/sequest.params > > > command "C:\Inetpub\tpp-bin\Out2XML.exe 043005_900c 1" failed: > > Operation not permitted > > > Command Successful > > > On Feb 18, 8:22 pm, Natalie Tasman <[email protected]> wrote: > >> Hi Kris, > > >> I'm glad that 4.1.1 on Windows with Apache has installed and is at > >> least somewhat working for you. > > >> I assume that you're using the TPP web interface (Petunia). When a > >> process is running, you'll see an option to refresh the page and see > >> the command's current output. Please copy and paste those command > >> outputs. It would be great if you would post back in two separate > >> threads (with different subjects) for each issue, so that we can keep > >> track of what's going on. > > >> Also, if you can give specifics about the type of instrument your > >> using and the size of the mzXML files used in your runs, that would be > >> useful. > > >> Best, > > >> Natalie > > >> On Feb 18, 2009, at 4:39 PM, Kris wrote: > > >>> Hi, > >>> I am NOT running TPP off of IIS. TPP will NOT work at all off of IIS. > >>> I have installed TPP 4.1 rev 1 using Apache on a different port. > >>> So, TPP should run the way it normally runs. > >>> However, I have found multiple issues. > >>> First, I will run SEQUEST through TPP using database search. On the > >>> 7th or 8th mzxml file I run, it will throw sequest errors that say > >>> Out2XML failed on the file using sequest.params > >>> This is not the params file I specified. > >>> I can try to copy the exact error for you, but I don't have the error > >>> message saved yet. > >>> The main issue is that peptide prophet does not work. > >>> I will run peptide prophet through analyze peptide and it gets stuck > >>> on the run PepxmlViewer command. There is an INDEX file that > >>> continuously gets bigger and bigger, but the command never finishes. > >>> Let me know what error messages I can submit to help you resolve this > >>> issue. > >>> -Kris > >>> On Feb 17, 12:39 pm, Natalie Tasman <[email protected]> > >>> wrote: > >>>> Hi Kris, > >>>> No one has been able to solve your specific program because no one > >>>> has > >>>> tried the exact setup that you have, which is trying to run Thermo's > >>>> Proteomics Browser Suite, requiring the TPP to use the unsupported > >>>> IIS > >>>> webserver. As you've found, the TPP can work with IIS, but we're not > >>>> able to actively support this configuration. > >>>> I would recommend that you simplify the situation and install the > >>>> TPP, > >>>> with the default Apache webserver, on a separate computer. Even if > >>>> it's an older machine you'll at least be able to isolate the issues > >>>> that you're experiencing. > >>>> Please let us know specifically what issues you've found with the > >>>> uninstaller. By default, the TPP won't delete its data directories. > >>>> Best wishes, > >>>> Natalie > >>>> On Mon, Feb 16, 2009 at 11:53 AM, Kris <[email protected]> wrote: > >>>>> Hi, > >>>>> I've posted many times, but I still haven't gotten my issues > >>>>> resolved. > >>>>> I have the Proteomics Browser Suite from Thermo on IIS on port 80 of > >>>>> my computer. > >>>>> I have tried the most recent version of TPP (4.1 revision 1) with > >>>>> Apache Webserver on port 8888, and pepxmlviewer was not working > >>>>> and I > >>>>> was getting random errors where it was saying cannot find parameters > >>>>> file sequest.params. But the parameters file I was using was not > >>>>> named > >>>>> sequest.params. > >>>>> I tried TPP 4.0 revision 2 on apache webserver 8888, but I was > >>>>> getting > >>>>> sequest27.exe errors when I would run database search. > >>>>> I tried running tpp on the IIS server already installed on port 80, > >>>>> but I the following errors on log in: > >>>>> Error Found! > >>>>> MD5_GEN:65280: A fatal error has been encountered. > >>>>> Error Found! > >>>>> NOLOGFILE: Cannot open /tmp/tpp_web.log for writing: Permission > >>>>> denied. > >>>>> Let me know if anyone has any suggestions for a stable windows > >>>>> version > >>>>> of tpp, how to configure it so it works with IIS or on a apache on > >>>>> port 8888. > >>>>> I'm also concerned that the uninstalls are not good enough because > >>>>> it > >>>>> does not seem that all of the files are being deleted. If anyone has > >>>>> any comments on incomplete uninstalls messing up new installations, > >>>>> let me know. > >>>>> -Kris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
