I checked in some code that yesterday that might address the issue. Perhaps you can send me your file and I can try to run my tool on it here? The FTP site is listed here: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F
Thanks, -David On Tue, Nov 8, 2011 at 11:47 AM, LW <[email protected]> wrote: > Hi David, > > Thanks. I tried the version from trunk and still got the segmentation > fault. > I ran it using: PTMProphetParser STY,80 interact.pep.xml > Is this the correct? > > I also ran gdb on it: > Program received signal SIGSEGV, Segmentation fault. > 0x00000000004d906e in > SpectraSTLibImporter::SpectraSTLibImporter(std::vector<std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, > std::allocator<std::basic_string<char, std::char_traits<char>, > std::allocator<char> > > >&, SpectraSTLib*, SpectraSTCreateParams&) () > > Could you commit your latest code > > Thanks, > LW > > On Oct 20, 10:41 am, David Shteynberg > <[email protected]> wrote: >> Hi LW, >> >> The version distributed in the release is perhaps a bit older than the >> one in SVN trunk. Have you tried building it from trunk? I know my >> version is working on Linux, if you build from trunk and it still >> doesn't work please let me know and I will commit my absolute latest >> code (that I've been testing without seg faults). >> >> Thanks, >> -David >> >> >> >> >> >> >> >> On Thu, Oct 20, 2011 at 9:56 AM, LW <[email protected]> wrote: >> > Hi David, >> >> > I got a segmentation fault when I tried to run the command-line linux >> > build. >> > Is there a working linux version? >> >> > Thanks, >> > LW >> >> > On Oct 19, 10:37 am, LW <[email protected]> wrote: >> >> Hi David, >> >> >> Thanks for the tip. I am interested in knowing how does PTMProphet >> >> algorithm differs from Ascore. >> >> Are they exactly same except implementation. >> >> Also, I can locate the PTMProphetParser in my linux build of TPP4.5.0. >> >> Can this be used instead of the window binary? >> >> It says the usage is PTMProphetParser <OPTIONS> <file1.pep.xml> >> >> May I know the options available? I am assuming it takes in >> >> PeptideProphet >> >> processed pep.xml. >> >> >> Thanks, >> >> LW >> >> >> On Oct 17, 4:29 pm, David Shteynberg >> >> >> <[email protected]> wrote: >> >> > Hi LW, >> >> >> > Yes I have used ascore with some success, although it is not >> >> > integrated with TPP and crashes sometimes on longer peptides. We have >> >> > a TPP integrated tool that is faster and as good or better than Ascore >> >> > from some initial testing. The tool is available on commandline only >> >> > at the moment and is not distributed with the installer yet. It is >> >> > called PTMProphet and you can get an initial Windows only version of >> >> > the test executable from this >> >> > link:http://dl.dropbox.com/u/21286225/PTMProphetParser.exe >> >> >> > Hope that helps, >> >> > -David >> >> >> > On Mon, Oct 17, 2011 at 4:11 PM, LW <[email protected]> wrote: >> >> > > Hi, >> >> >> > > I am wondering if anyone has use the ascore for >> >> > > phospho site localization on XTandem/TPP processed data. >> >> > > The software in Gygi lab seems to be based on sequest dta/out output. >> >> >> > > Thanks, >> >> > > LW >> >> >> > > -- >> >> > > You received this message because you are subscribed to the Google >> >> > > Groups "spctools-discuss" group. >> >> > > To post to this group, send email to >> >> > > [email protected]. >> >> > > To unsubscribe from this group, send email to >> >> > > [email protected]. >> >> > > For more options, visit this group >> >> > > athttp://groups.google.com/group/spctools-discuss?hl=en. >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group >> > athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
