Did you try adjusting the Apache timeout parameter as Brian suggested? Here's a description of what that parameter controls on the webserver: http://httpd.apache.org/docs/2.2/mod/core.html#timeout
A search for 'apache timeout' in this google group brings up this thread with some information on how to change that parameter: http://tinyurl.com/nrr58v - Jimmy Antonio wrote: > 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 -~----------~----~----~----~------~----~------~--~---
