Magnus, The expectation value calculation does not depend on the batch size at all. It's calculated for each spectrum query and is only a function of the spectrum and its peptide search space (where search space is defined by the database and the search parameters).
- Jimmy On Tue, Mar 4, 2014 at 2:12 AM, [email protected] < [email protected]> wrote: > Hi Jimmy, > > Many thanks - the "spectrum_batch_size" trick worked! Are the results > (e.g. the expectation values) dependent on the batch size? > > > Cheers, > > Magnus > > > On Monday, 3 March 2014 19:05:21 UTC+1, Jimmy Eng wrote: > >> Mangus, >> >> There's something broken with our latest Comet 2013.02 rev. 2 release >> under Windows. We attempted to address large memory search performance, >> which appeared to work fine in our limited testing, but we definitely broke >> something else in the process and are actively working on addressing this >> issue now. >> >> The current suggested work-around would be: >> a). make use of the "spectrum_batch_size" parameter; set it to some >> value, say 3000 or 5000 to allow you to process your data by searching >> smaller batches of spectra at a time >> b). revert the Comet binary to the previous 2013.02 rev. 1 release. >> >> - Jimmy >> >> >> On Mon, Mar 3, 2014 at 9:46 AM, [email protected] < >> [email protected]> wrote: >> >>> Dear TPP developers and users, >>> >>> I took the the new Comet in TPP 4.7 (POLAR VORTEX) out for spin, but >>> keep getting errors like "Error - >>> CometMemMgr::CometMemAlloc(pdTmpFastXcorrData[1374])" >>> and "Operation not permitted" when searching an mzXML made from some 5 GB >>> Orbitrap E. coli data. This mzXML file works fine with both X!Tandem and >>> SpectraST. To get a parameter file, I created one with "comet -p". >>> >>> When I search a tiny mzXML file with one MS1 and three MS2 spectra I >>> created myself, it works, and I get reasonable results. But I have tried it >>> with reasonably small ion trap datasets of <100 MB, I get the errors as for >>> the 5 GB Orbi data. >>> >>> Any suggestions? Should I allocate more memory to comet somewhere? >>> >>> >>> Cheers, >>> >>> Magnus >>> >>> -- >>> 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. >>> 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. > 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. > 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. 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. For more options, visit https://groups.google.com/groups/opt_out.
