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]<javascript:> > > 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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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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