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 <j...@systemsbiology.org> 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 <j...@systemsbiology.org> 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 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 -~----------~----~----~----~------~----~------~--~---
