It did not end up for me. I am using comet (not tandem) on a windows machine and sometimes I got "*file not found:* not created or deleted?" I have reduced the filename to just a number. My output files are always created in the parameter folder. Is there a possibility to use a differnt folder for it ? I am using TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686). Norbert
On Monday, July 22, 2013 11:18:19 PM UTC+2, Kierstin wrote: > > It ended up being a parameters issue. Now it's working. Thanks so much! > > On Monday, July 22, 2013 4:39:50 PM UTC-4, [email protected] > wrote: >> >> Kierstin, >> >> You might want to take a 2nd look at what parameters you are also using >> for X!Tandem. I find it pretty useful to use the API documentation >> <http://www.thegpm.org/tandem/api/index.html> as a guide. What platform >> are you running TPP on, Windows? and what version of TPP are you using? >> >> -Joe >> >> >> >> On Mon, Jul 22, 2013 at 11:35 AM, Kierstin <[email protected]> wrote: >> >>> Thanks Joe! >>> >>> I checked out my spectrum in Pep3D and it looks fine! For the database >>> input, I'm using the FASTA file, I'm just using the standard Human >>> database, and for the parameters, the default tandem parameters file. I've >>> gone through it and don't see any special characters. If you have any >>> other suggestions, I'll definitely try them! >>> >>> Thanks, >>> >>> Kierstin >>> >>> >>> On Monday, July 22, 2013 12:23:28 PM UTC-4, [email protected] >>> wrote: >>> >>>> Kierstin, >>>> >>>> Try checking your input to X!Tandem. Make sure the database doesn't >>>> have any "bad" sequences in it. Often times special characters sneak into >>>> the file and can cause X!Tandem to crash. Also take a look at your >>>> spectrum -- can you see the input file in Pep3D? >>>> >>>> -Joe >>>> >>>> >>>> On Mon, Jul 22, 2013 at 9:20 AM, Kierstin <[email protected]> >>>> wrote: >>>> >>>>> Hi! >>>>> >>>>> Thanks for the suggestion! I removed all of the spaces and alternate >>>>> characters and am still getting the same error messages. Is there >>>>> anything >>>>> else I should try? Should I recheck my parameters file? >>>>> >>>>> Thanks! >>>>> >>>>> Kierstin >>>>> >>>>> >>>>> - c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem (*file >>>>> not found:* not created or deleted?) >>>>> - c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem.pep.xml >>>>> (*file not found:* not created or deleted?) >>>>> >>>>> >>>>> >>>>> Command 1 *[Mon Jul 22 12:11:18 2013] * [ Show / Hide ] >>>>> >>>>> run_in c:/Inetpub/wwwroot/ISB/data/Tandem; c:\Inetpub\tpp-bin\tandem >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem.params >>>>> >>>>> ------------------------------ >>>>> >>>>> X! TANDEM 2010.10.01.1 (LabKey, Insilicos and ISB) >>>>> >>>>> Loading spectra . >>>>> This application has requested the Runtime to terminate it in an unusual >>>>> way. >>>>> Please contact the application's support team for more information. >>>>> >>>>> command "c:\Inetpub\tpp-bin\tandem >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem.params" >>>>> failed: No such process >>>>> >>>>> *Command FAILED* >>>>> >>>>> >>>>> Command 2 *[Mon Jul 22 12:11:19 2013] * [ Show / Hide ] >>>>> >>>>> run_in c:/Inetpub/wwwroot/ISB/data/Tandem; c:\Inetpub\tpp-bin\Tandem2XML >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem.pep.xml >>>>> >>>>> ------------------------------ >>>>> >>>>> Failed to open input file >>>>> 'c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem'. >>>>> >>>>> command "c:\Inetpub\tpp-bin\Tandem2XML >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem >>>>> c:/Inetpub/wwwroot/ISB/data/Tandem/MS13668QE_sample2.tandem.pep.xml" >>>>> failed: Operation not permitted >>>>> >>>>> *Command FAILED* >>>>> >>>>> On Wednesday, July 17, 2013 7:28:22 PM UTC-4, Jimmy Eng wrote: >>>>> >>>>>> Along these lines, everyone should simply avoid any symbols in >>>>>> directory and file names. There are some character symbols that are OK >>>>>> (I >>>>>> tell folks to use dash '-' and underscore '_' only besides letters and >>>>>> numbers) but it's best to avoid them all if you don't know which ones >>>>>> will >>>>>> work. >>>>>> >>>>>> >>>>>> On Wed, Jul 17, 2013 at 3:28 PM, Brian Hampton <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> Well, I could be wrong, but that space in the directory name is >>>>>>> probably the culprit. I would rename the directory .../data/X! Tandem >>>>>>> to >>>>>>> something without a space in it. Just call it .../data/tandem instead. >>>>>>> >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Brian >>>>>>> >>>>>>> Brian Hampton >>>>>>> Protein Analysis Lab >>>>>>> Center for Vascular and Inflammatory Diseases >>>>>>> University of Maryland School of Medicine >>>>>>> 800 West Baltimore Street Rm 307 >>>>>>> Baltimore MD 21201 >>>>>>> V: 410-706-8207 >>>>>>> F: 410-706-8234 >>>>>>> >>>>>>> >>>>>>> On Wed, Jul 17, 2013 at 5:24 PM, Kierstin Schmidt < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Hi! >>>>>>>> I am a new user of TPP. I am trying to load my mzXML files to be >>>>>>>> searched by X! Tandem, and I keep getting the following errors. If >>>>>>>> anyone >>>>>>>> has advice, it would be greatly appreciated! >>>>>>>> >>>>>>>> Thanks! >>>>>>>> >>>>>>>> Kierstin >>>>>>>> >>>>>>>> >>>>>>>> "c:/Inetpub/wwwroot/ISB/data/X! Tandem/MS138QE_sample2.tandem.pep.xml >>>>>>>> (*file not found:* not created or deleted?) >>>>>>>> >>>>>>>> Followed by >>>>>>>> >>>>>>>> run_in c:/Inetpub/wwwroot/ISB/data/X!Tandem; >>>>>>>> c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem.params >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> >>>>>>>> X! TANDEM 2010.10.01.1 (LabKey, Insilicos and ISB) >>>>>>>> >>>>>>>> Loading spectra . >>>>>>>> Failed to open: "c:/Inetpub/wwwroot/ISB/data/X!Tandem" >>>>>>>> The input parameter file "c:/Inetpub/wwwroot/ISB/data/X!Tandem" could >>>>>>>> not be located. >>>>>>>> Check the file path name and try again. >>>>>>>> >>>>>>>> >>>>>>>> An error was detected while loading the input parameters. >>>>>>>> Please follow the advice above or contact a GPM administrator to help >>>>>>>> you. >>>>>>>> command "c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem.params" failed: Unknown error >>>>>>>> >>>>>>>> *Command FAILED* >>>>>>>> >>>>>>>> >>>>>>>> Command 2 *[Wed Jul 17 17:11:38 2013] * [ Show / Hide ] >>>>>>>> >>>>>>>> run_in c:/Inetpub/wwwroot/ISB/data/X!Tandem; >>>>>>>> c:\Inetpub\tpp-bin\Tandem2XML c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem.pep.xml >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> >>>>>>>> c:\Inetpub\tpp-bin\Tandem2XML(TPP v4.5 RAPTURE rev 2, Build >>>>>>>> 201202031108 (MinGW)) >>>>>>>> Usage: c:\Inetpub\tpp-bin\Tandem2XML <input-file> [<output-file>] >>>>>>>> >>>>>>>> command "c:\Inetpub\tpp-bin\Tandem2XML c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem c:/Inetpub/wwwroot/ISB/data/X! >>>>>>>> Tandem/MS138QE_sample2.tandem.pep.xml" failed: Operation not permitted >>>>>>>> >>>>>>>> *Command FAILED* >>>>>>>> >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "spctools-discuss" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to [email protected]. >>>>>>>> To post to this group, send email to [email protected]. >>>>>>>> >>>>>>>> Visit this group at http://groups.google.com/group/spctools-discuss >>>>>>>> . >>>>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "spctools-discuss" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to [email protected]. >>>>>>> To post to this group, send email to [email protected]. >>>>>>> >>>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>>> >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >> >> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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