Hi Anne, Sorry for the late response. This kind of error means the Java Virtual Machine itself crashed. That is quite unusual - I suppose it could be caused by some problem in linking the R-related libraries to the Java Virtual Machine. But I am not 100% sure. Actually, we recently changed the way R modules are used in MZmine, so your problem should be automatically fixed in the upcoming MZmine version (2.15).
In the meantime, I would suggest to use a different deconvolution module, e.g. Local minima search instead of the XCMS module. By the way, it is not a good idea to set the "Min time span" to 0 for the Chromatogram builder - you will end up with a huge number of noise features. That's why your project file gets so big. Use a reasonable minimum according to the width of your chromatographic peaks. Similarly, if you set the noise level to 1E4 in the Mass detection module, it does not make sense to set the min height to 1E2 in the Chromatogram builder. Again, use a reasonable minimum according to the height of your chromatographic peaks. Best regards, Tomas On Wed, Jul 1, 2015 at 5:28 AM, Anne O'Connor <oconno...@cardiff.ac.uk> wrote: > Hi there, > > I really hope you can help with an error I am getting using MZmine. I am > running quite large Thermo files through mass detection (ok), chromatogram > builder (ok) and chromatogram deconvolution (crashes here). I have put all > the info that the manual says to include and all raw files (plus system info > file, error log and R info) on dropbox here: > https://www.dropbox.com/sh/mcv4pirjqpezqa8/AACjyeEem2BPnTxH8wEorZjra?dl=0 > > I have never used MZmine before, so its quite possible that I have set > parameters incorrectly or done something very silly!! > > NOTE: The data files I have provided to you are unpublished data and need to > be kept confidential. > > Any problems accessing the data on dropbox or if you require any further > info, please email me. > > Thanks, > Anne > > > Anne O'Connor Ph.D > Bioinformatics Research Associate > > Institute of Infection and Immunity > School of Medicine > Cardiff University > Tenovus Building > Heath Park > Cardiff > Anne O'Connor Ph.D > Bioinformatics Research Associate > > Institute of Infection and Immunity > School of Medicine > Cardiff University > Tenovus Building > Heath Park > Cardiff > CF14 4XN > > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
