I forgot to mention the mzxml files for this run ranged from 15-25 mb. And I don't know the mass spec used because the spectrum I run are from a database of other people's mass spectra.
And sorry I forgot to start a new thread, Kris On Feb 20, 11:11 am, Kris <[email protected]> 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 -~----------~----~----~----~------~----~------~--~---
