Hi Chiarina, I am glad to hear that your problem is solved.
> @Tomas, well, I was originally using MZmine 1.97, because with > MZmine 2.0 I was unable to open .RAW files at all (I found this > initially strange given the two versions were installed on exactly the > same computer and so at the time abandoned using later versions). The > max no. of .RAW files I could open with 1.97 produced .scans files of > 6.41gb total (208 .RAW files). I copied an extra 3.97gb of data into the > temp folder manually as a test as you suggested and this operation was > fine, so the temp folder itself didn't have a restriction there. I also > found, strangely, that if I converted the .RAW files to .cdf or mzXML > then I could open all 280 of my sample files (27gb .cdf files, or > 6.7gb .mzXML files and 10.6gb scans files). > In the course of learning about the mzXML format and how to convert .RAW > files (I used msconvert on my computer as I read it is the latest > recommended version over ReAdw) - I had to make some updates to my > computer to get msconvert to run - installing .NET 3.5 sp1, a C + + > redistributable, MSFileReader.exe, loading various .dll libraries etc, > so I don't know which of these things made a difference, but now I find > that I can open .RAW files with MZmine 2.0 and 2.2. And with these > versions I can in fact open all 280 .RAW files. So - my problem solved! I think MZmine 1.97 had a memory leak in the rawdump.exe module which is responsible for the binding to the XCalibur COM library. That is why after opening certain number of files, it runs out of memory, even when your JVM still has enough memory left (rawdump.exe is not using JVM memory, it is an external Windows process). You should not use MZmine 1.97, it is evil. The reason why you could not open RAW files with MZmine 2.x was that it uses the MSFileReader library (unlike MZmine 1.97, which binds to XCalibur). The reason for this change is obvious: MSFileReader is free, while XCalibur is not. The fact that MZmine 2.x needs MSFileReader is described in the manual. > > I would like to test the system better with your 'creating lots of .RAW > files suggestion' but I'm afraid I don't know how to do it. I tried to > use the MZmine filter but then you can't export your cropped files as > individual .RAW files, just have them within the project, if I am > right! Even if I retrieved the cropped files from my .mzmine project > file then they are no longer in .RAW format so not a true test....as I > mentioned before MZmine 1.97 seemed to be able to handle lots of .mzXML > fine. You can just use the Windows Explorer to make many copies a single RAW file. But I think it is not necessary now, since the problem is already solved. > ps in the manual for 2.0 and 2.2 it says the thing needed for .RAW data > import is http://sjsupport.thermofinnigan.com/public/detail.asp?id=624 > which is called 'Chromobj.dll' > but isn't it this link, to MSFileReader.exe?? > http://sjsupport.thermofinnigan.com/public/detail.asp?id=703 Yes the correct link is to the MSFileReader, unfortunately Thermo keeps changing the link whenever they release a new version (before January, http://sjsupport.thermofinnigan.com/public/detail.asp?id=624 was a download page for MSFileReader). The MZmine 2.3 manual will be updated with the correct link (http://sjsupport.thermofinnigan.com/public/detail.asp?id=703). Best regards, Tomas =============================================== 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 ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
