Yes, just replace Comet with an updated linux binary. The file comet.2016012.linux.exe in the zip file is what you want. If that binary does not run, let me know and I can compile an Ubuntu binary for you or you can compile from sources. You'll have to identify where the existing Comet lives in your Ubuntu install.
On Sun, Jun 12, 2016 at 11:49 PM, 钟传奇 <[email protected]> wrote: > 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 a version of Comet (release 2014.02 rev. 2) that's outdated by nearly 2 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. > -- 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.
