Hi Jimmy, OK, done it. No problem, the command were successfull, all finished, th eTPP window indicated that the command was sucessfull and is finished. i can open the basename.pep on TPP and all seens OK. What next?
Antonio On Jul 8, 12:33 pm, Jimmy Eng <[email protected]> wrote: > Antonio, > > Can you try this. Replace "basename" with one of your RAW/mzXML file > base name (i.e. <basename>.mzXML) > > Collate data as > > c:/Inetpub/wwwroot/ISB/data/AAS/basename.mzXML > c:/Inetpub/wwwroot/ISB/data/AAS/basename/ contains dta/out > c:/Inetpub/wwwroot/ISB/data/AAS/sequest.params > > Then in a command prompt run > > cd c:/Inetpub/wwwroot/ISB/data/AAS/ > Out2XML basename 1 > > This should create basename.pep.xml in the AAS directory. This simple > exercise is just to confirm that it runs through correctly and the > process finishes. The next thing to try is to repeat the above data > structure but try the pepXML conversion in the GUI. Hopefully this > isolates whether you're experiencing a pepXML conversion problem or a > GUI problem. > > - Jimmy > > > > Antonio wrote: > > Hi Jimmy, > > > I run Sequest from Bioworks on our computer cluster, and then transfer > > the files to the local machine running TPP, so yeas I had the c:/ > > Inetpub/wwwroot/ISB/data/AAS/test/ > > With the out-and dta- files in it. > > I have attempted to run Sequest from TPP and I had the same problem; > > the dta and out files are created, but the command indicates that is > > still running. The problem occurs whether I send a few files or a > > single one. But I have more than one file on the queue, the command > > will not proceed to the next file. I can run Sequest from Bioworks on > > the local machine without any problems. > > > On Jul 2, 6:55 pm, Jimmy Eng <[email protected]> wrote: > >> Antonio, > > >> That warning about not being able to open the mzXML file is not > >> indicative of the underlying problem. It is truly just a warning and > >> the analysis process is capable of finishing correctly even if the > >> corresponding mzXML file is missing. > > >> The important question that's not clear from your description below is > >> how did you run the Sequest search? Did you run it separately via > >> Bioworks or did you run the search through the TPP? Although helpful > >> but not required, it doesn't seem like you did the latter. Do you have > >> a directory (e.g. c:/Inetpub/wwwroot/ISB/data/AAS/test/) that has the > >> Sequest .out files in it? > > >> - Jimmy > > >> Antonio wrote: > >>> I have installed TPP v4.2 on windows XP. I have created the mzXML > >>> datafiles from my Sequest search. Now I'm making the corresponding > >>> pepXML files. I see that the first file is being created, it seems > >>> that is finished but I see the following warming message at the end of > >>> the “Output so far” field: > >>> warning: cannot open mzXML file "c:/Inetpub/wwwroot/ISB/data/AAS/ > >>> test.mzXML" for reading MS instrument info and scan times. > >>> And the command status window indicates that the command is still > >>> running. Is it? I do not see the file increasing in size. I can open > >>> the pepxml file, although IE indicates that there is an error on page. > >>> It seems to me that the program is stuck and is not progressing to > >>> next task: the creation of the next pepXML file. Solutions? > >>> Thanks, > >>> Antonio- Hide quoted text - > >> - Show quoted text -- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
