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]: > >> 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 spctools-discu...@**googlegroups**.com. >>>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>>> >>>>>> Visit this group at http://groups.google.com/**group** >>>>>> /spctools-discuss <http://groups.google.com/group/spctools-discuss>. >>>>>> For more options, visit >>>>>> https://groups.google.com/**grou**ps/opt_out<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 spctools-discu...@**googlegroups**.com. >>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>> >>>>> Visit this group at http://groups.google.com/**group** >>>>> /spctools-discuss <http://groups.google.com/group/spctools-discuss>. >>>>> For more options, visit >>>>> https://groups.google.com/**grou**ps/opt_out<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 spctools-discu...@**googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.**com. >>> Visit this group at >>> http://groups.google.com/**group/spctools-discuss<http://groups.google.com/group/spctools-discuss> >>> . >>> For more options, visit >>> https://groups.google.com/**groups/opt_out<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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