Hi Jimmy, I have repeated the process from TPP. The command gets stuck either after sending the Sequest search or creating the pepXML file. I might have to reinstall pearl and TPP. Antonio
On Jul 9, 2:41 pm, Antonio <[email protected]> wrote: > Ok Jimmy, > Thank you very much for your help. > I'll repeat the entire process from TPP and I will let you know the > result. > Regards, > Antonio > > On Jul 9, 2:18 pm, Jimmy Eng <[email protected]> wrote: > > > > > I guess the next step is to repeat the pepXML conversion from the GUI > > and see if the GUI reports that the command completed successfully. If > > it does, organize a couple of search directories using the same > > structure and repeat the pepXML conversion. Still getting stuck or is > > the processes reported to be completed? > > > If if looks like the first pepXML file is generated/completed but the > > interface thinks the command is still running, I'm going to need Luis to > > chime in on what to look for as I've exhausted the bits I have knowledge > > of. So let us know what happens when you try the above. > > > - Jimmy > > > Antonio wrote: > > > 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 -- 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 -~----------~----~----~----~------~----~------~--~---
