Philip, I'm guessing you're specifying a small "fragment_bin_tol" value for the high-res ms/ms spectra. This causes Comet (not all capitalized) to use a ton of memory and you're just running out of memory.
On the following UWPR SEQUEST page, there's a table correlating a set of fragment_bin_tol settings vs. # input spectra vs. memory used: https://proteomicsresource.washington.edu/sequest_release/release_201201.php These numbers apply to Comet as well. To address the problem, run smaller searches i.e. run Comet on a subset of your input spectra. You can do this either with the "scan_range" parameter in the params file or simply invoke the searches such as comet yourfile.mzXML:1-3000 comet yourfile.mzXML:3001-6000 comet yourfile.mzXML:6001-9000 Your going to get multiple outputs if you do this which will need to be handled. Splitting searches and managing results is something that some script should do for you; some day I'll throw some simple windows and linux example scripts on the Comet website for users. Hopefully we'll have a workaround to address the memory use for these small fragment_bin_tol values in the semi-near future (thanks to Mike Hoopmann here who has implemented sparse matrix support in the code which I'm actively working with now). - Jimmy On Wed, Jan 16, 2013 at 11:05 AM, Philip Brownridge < philip.brownri...@gmail.com> wrote: > Hello all, please can I apologise if I have posted this in the wrong > group, but I can't find a COMET group and there are other COMET postings > here so I hope someone can help me! I'm trying to use some QExactive data > with Comet and I keep getting either a calloc error message or a message > saying there is no search to perform. I can get COMET searches to work on > LTQ Orbitrap data but not QExactive. I have been using Proteowizard to > convert the RAW files to mzML. I'm using the default params file with high > resolution fragment ion parameters. > Please if anybody is using COMET with QExactive data please could they let > me know where i'm wrong! > thanks in advance, > Philip > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/Jr5k5f4wcY0J. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
