Hi Jimmy, I also want to ask how to update Comet in TPP in Ubuntu system. Does Comet work if I just replaced the Comet file like you mentioned in the email.
Thanks. On Mon, Jun 13, 2016 at 2:24 PM, Jimmy Eng <[email protected]> wrote: > Vijay, > > Update to the latest Comet and try again. There's a good chance it won't > solve your problems but there's no point in investigating search issues for > a version of Comet (release 2014.02 rev. 2) that's outdated by nearly 2 > years. > > To update your Comet binary, go to comet-ms.sourceforge.net and click on > the "download" tab. Then click on the file named > "comet_binaries_2016012.zip" to download the most recent release (version > 2016.01 rev. 2). Extract the file named "comet.2016012.win64.exe" from the > archive. Find your current Comet binary (should be at c:\inetpub\tpp-bin\ > comet.exe) and replace it with the binary in this zip file (rename comet > .2016012.win64.exe to c:\inetpub\tpp-bin\comet.exe). Also update your > Comet search parameters file comet.params with a version appropriate for > release 2016.01 rev 2. You can find updated example comet.params files at > http://comet-ms.sourceforge.net/parameters/parameters_201601/. If you > download one of those, such a the file comet.params.high-low for high-res > MS1 and low-res MS2 data, just remember to change the name to simply > "comet.params" and update any parameter settings as needed. > > Try your search again with the latest Comet and see if it magically fixes > your problem. In the event that it doesn't fix the problem, send me one of > the problem mzXML files, your comet.params, your sequence database, and > info on how much RAM your computer has. As email likely won't work for > such large files, use a service like Dropbox or OneDrive to get me the > files and I'll investigate. > > - Jimmy > > On Sun, Jun 12, 2016 at 11:09 AM, Vijay Kumar <[email protected]> > wrote: > >> Hi, >> I am running comet database search for my 15 fraction of mzXML data file >> from WATERS QTOP. Out of 15 fractions only 5 fractions command are >> success, remaining fraction has the following error >> >> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data& c:\Inetpub\tpp-bin\comet >> -Pc:/Inetpub/wwwroot/ISB/data/parameters/comet.params >> -Nc:/Inetpub/wwwroot/ISB/data/parameters/17052016_NISHAD_ITRAQ_1 >> -Dc:/Inetpub/wwwroot/ISB/data/parameters/Chicken.fa >> 17052016_NISHAD_ITRAQ_1.mzXML * >> >> Warning - invalid parameter found: precursor_tolerance_type. Parameter >> will be ignored. >> Warning - invalid parameter found: require_variable_mod. Parameter will be >> ignored. >> Warning - invalid parameter found: mass_offsets. Parameter will be ignored. >> Warning - invalid parameter found: add_U_selenocysteine. Parameter will be >> ignored. >> Comet version "2014.02 rev. 2" >> >> Search start: 06/12/2016, 11:21:12 PM >> - Input file: 17052016_NISHAD_ITRAQ_1.mzXML >> - Load and process input spectra >> >> *Command FAILED* >> RETURN CODE:65280 >> >> Kindly help some one what could be the reason?how can i solve this >> problem? >> >> -- >> 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 https://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. > 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 https://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. 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
