Hello Jimmy, thank you very much for your quick reply! You're completely correct about the fragment bin value, when I ran Comet (thank you for name guidance) using the LTQ settings it worked fine! When I ran it on the high resolution settings with task mamager on, I saw that I was getting the calloc error at about 2Gb of memory. I'm running Comet on a win7-64bit machine with 24Gb of memory and the program is called comet-win32, please could you tell me whether it would be possible to recompile Comet for win64 and perform larger searches? Sorry if this is a naive question, i'm very much a beginner when it comes to code. thank you again, Philip
On Wednesday, 16 January 2013 19:55:58 UTC, Jimmy Eng wrote: > > 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 > <[email protected]<javascript:> > > 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 >> [email protected]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/7G1xmAbgOskJ. 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.
