fwiw, the command line tests were successful. Brian Pratt wrote: > 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 - >> >> >> >> > > > > > > >
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