Jimmy, Thanks for that info. Sounds great. I'll proceed based on the knowledge that'll be available.
Cheers, DT On Monday, April 1, 2013 4:43:40 PM UTC-5, Jimmy Eng wrote: > > Dave, > > Mike Hoopmann implemented a nice fix for searches using small bins. The > sources current in Comet SourceForge trunk should be fully functional. One > new parameter entry is titled "use_sparse_matrix" (see Comet version > 2013.01 params in link below) which controls whether or not the sparse > matrix data representation is used. For small bins, this not only > addresses the memory use but those searches are also a little faster. > > http://comet-ms.sourceforge.net/parameters/parameters_201301/ > > There's one other little feature I'd like to add before putting out > another official release but the sparse matrix data representation to deal > with this issue (memory use and small bin sizes) is the major feature in > the next version. When the next release happens, I'll document memory use > and compare small vs. large bins on high res data (among other analysis). > > - Jimmy > > > On Mon, Apr 1, 2013 at 2:33 PM, Dave Trudgian < > [email protected] <javascript:>> wrote: > >> 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<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<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 spctools-discu...@** >>>>> googlegroups.com. >>>>> For more options, visit this group at http://groups.google.com/** >>>>> group/spctools-discuss?hl=en<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] <javascript:>. >> >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss?hl=en >> . >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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