ps my datafiles are centroided XCalibur .RAW files, with about 40 mins long elution (= 30MB each). I am guessing Gözde's files are much smaller (I hope for their sake :-) C
On 06/05/2011 15:37, Chiarina Darrah wrote: > Hi! Further to the below message, I wanted to have a better > understanding of sample number limits; at the moment in my lab we are > unable to get mzmine to open more than about 200 samples at once. > Attempting any more gets the error message: "There is an error in the > RAW file, please check the log file" But the same RAW files can be > imported successfully if mzmine is restarted, so the files are not > corrupted or anything. The log file , after the "..FINEST....Xcalibur > 2.0 interface initialized" just says "...SEVERE...Unable to open > XCalibur RAW file". > > 200 samples was an improvement from about 120 samples (the previous > limit before getting identical error messages) - when I realised that > I just didn't have enough space on my drive for all the .scans files > being generated in the TEMP folder mzmine was using. Having increased > this to many GB more than needed, then I could indeed open more files. > But not as many as I was expecting. Now, at 200 samples, I have plenty > of space left on the drive (18GB), and I increased the JVM to the > 1.3GB max for the 32-bit system I'm using, and it has 900 MB free when > not performing tasks, and even when performing tasks it is not coming > close to maxing out. > > So my question is, what further avenues do I have to increase the no. > of samples - what other things are limiting the no. of samples I can > open? > I have a total of 280 samples - it's really annoying to do two batches > because then I have to do the very long-winded downstream processes > twice, working with two separate peak lists when I just want to work > with one within mzmine (I have to work within mzmine as far as I can > tell because I am inspecting MSMS spectra). > > A workaround would be to be able to merge two peaklists - but as far > as I can see, I wouldn't be able to work with MSMS data from all the > peaks on the peak lists unless I had all the raw data open in my > project - which, as I explained above, I can't currently do. > > Thanks for your time! > > Chiarina Darrah > > > > > > > Hi Gözde, > > I have never tried analyzing so many samples at once using MZmine. > There may be a lot of places in MZmine where the code is not optimized > for such high-scale analysis. > Also, it depends on the characteristics of your data (high vs low > resolution, centroided vs continuous spectra etc.). > You may need more RAM than 16GB (there are computers with 1TB of RAM > or more). > You may also split the analysis into separate batches. > > Tomas > > > On Mar 3, 2011, at 11:07 PM, Gözde Gürdeniz wrote: > > > We have been processing the UPLC-QTOF samples with MZmine and it has > worked pretty until now J > > > > However now, I have huge number of samples 5000. I tried to increase > the RAM that MZmine is using according to capacity of my computer > (16 GB RAM that I have). I could manage to process only 1500 samples. > I am working on windows and I guess I can increase the amount of > virtual memory for the use of MZmine by Linux. > > > > Do you think I should go for Linux or is there any other way to > solve this problem of 5000 samples or it does not seem realistic? > > > > > > > > M. Sc, PhD-student > > Gözde Gürdeniz, > > Group of Preventive Nutrition, > > Department of Human Nutrition, > > University of Copenhagen, > > Rolighedsvej 30, DK-1958 Frederiksberg > > Copenhagen-Denmark > > > > E-mail: gozg@... > > Cell Phone: (+45) 29176389 > > > ------------------------------------------------------------------------------ > > Free Software Download: Index, Search & Analyze Logs and other IT > data in > > Real-Time with Splunk. Collect, index and harness all the fast > moving IT data > > generated by your applications, servers and devices whether > physical, virtual > > or in the cloud. Deliver compliance at lower cost and gain new business > > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > > Mzmine-devel mailing list > > Mzmine-devel@... > > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology > 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan > TEL: +81-98-966-8684 > -- ================================================================== Chiarina Darrah Tel:+32 (0)9 331 38 85 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM ch...@psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== ------------------------------------------------------------------------------ WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
