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 - --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
