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 from www.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 <ntas...@systemsbiology.org> 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 <ntas...@systemsbiology.org> >>> 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 <ktrunc...@gmail.com> 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 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 -~----------~----~----~----~------~----~------~--~---
