Hello Norbert, The error you are seeing suggests an upstream problem that should be in the error log. Without seeing the complete output it is difficult to tell, but I suspect a problem with the mzML/mzXML file.
The output files are now, always output to the directory containing the parameters. To change the output directory create a directory of your choice and copy the parameter file to this directory. Cheers, -David On Thu, Jan 1, 2015 at 5:59 AM, Norbert Mehlmer <[email protected]> wrote: > 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. > 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/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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