Hi Philip, Sorry to drag up an old thread, but I wondered if you had info about the effects on results of limiting Comet memory usage by using a large bin, vs using the 64-bit binary and small bin?
We are primarily working with QExactive data here. I was thinking of adding Comet to our pipeline, and checking on the bin-size effect on results - but cheekily wondered if you or anyone else have any feeling for this? Cheers, Dave Trudgian On Thursday, January 17, 2013 6:56:11 AM UTC-6, Philip Brownridge wrote: > > 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]> 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]. >>> 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 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 http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
