Agreed - the proper test is to invoke it from the command line and see if it actually does complete eventually. An infinite loop bug is always a possibility.
Brian -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Jimmy Eng Sent: Wednesday, July 15, 2009 1:02 PM To: [email protected] Subject: [spctools-discuss] Re: pepXML 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 -~----------~----~----~----~------~----~------~--~---
