Jimmy, Just to clarify: the timeout occurs both during the Sequest search and also during the pepXML conversion. I haven't gotten the time to reinstall the software in this computer; I hope I can do it sometime this week. I'll post my findings once this is completed. Again, many thanks you for your help, Antonio
On Jul 15, 3:02 pm, Jimmy Eng <[email protected]> wrote: > It's hard to tell from the dialogue whether the timeout is occuring > during the search phase or during the pepXML conversion, which are two > different tasks invoked by the GUI. I want to think it's the latter > since Antonio mentions that "pepXML conversions apparently have > completed". And if this were the case, I'm not sure that Apache time > out is the culprit since these conversions shouldn't take forever. > Anyways, that looks like a handy feature for the next GUI release. > > Brian Pratt wrote: > > That can happen on long searches - Apache times out, leaving your session > > stuck waiting for a message that never arrives. You can adjust your Apache > > config for longer timeouts (look through this group's archives for info on > > that). > > > The next TPP GUI release features a button I added for the user to be able > > to tell the GUI "no really, it's done, let's go look at the results". > > > -----Original Message----- > > From: [email protected] > > [mailto:[email protected]] On Behalf Of Jimmy Eng > > Sent: Wednesday, July 15, 2009 10:26 AM > > To: [email protected] > > Subject: [spctools-discuss] Re: pepXML > > > Antonio, > > > Hopefully Luis or someone else more familiar with the GUI will chime in > > and help you debug why it appears to not recognize that the pepXML > > conversions apparently have completed but it still thinks they're > > running. There are log files somewhere that the GUI looks at that would > > be the starting point to figuring out your mystery. > > > - Jimmy > > > Antonio wrote: > >> Hi Jimmy, > >> I have donne it from TPP. the program still gets stuck. pepXML files > >> are created and Sequest serach is performed, but the program reports > >> that the command is still running. > >> I might have a problem with the installation. I will have to reinstall/ > >> rebuild the computer. > >> 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 -~----------~----~----~----~------~----~------~--~---
