Hi, I think you should think about a 64bit PC with 64bit OS. This should solve your issue for the moment.
Cheers Marco Am 06.05.2011 16:22, schrieb Chiarina Darrah: > 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. 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