G'day, It's curious that performance was significantly faster with JRE 6.0 vs. 7.0, and that it fixed the bug. Do you see this improvement for all MZmine operations or just those involving XCMS?
As for the time taken for XCMS peak deconvolution, it's difficult for me to comment as you don't say how many peak-lists you're processing, how many chromatograms they contain, and how many data points are in each chromatogram. Your parameters seem reasonable. When setting deconvolution parameters do you use the preview facility? This applies XCMS to individual chromatograms. How long does it take to process a single chromatogram? On my set up it takes less than one second for individual chromatograms from the sample-2.3 data set (http://sourceforge.net/projects/mzmine/files/sample%20data%20set/). Regards, Chris. On 11/07/12 03:13, Raghavendra Gunnaiah wrote: > Dear Chris, > It works well with JRE 6.0 update 33 and the program runs quite fast compared > to the one with JRE 7.0. > But still it takes more than 2 hours for peak deconvolution using > xcms(wavelets) method. With JRE 7.0., it was more than 6 hours. > Parameters set for xcms(wavelets): wavelets scales (0.2-5.0 min) and peak > duration (0.2-1.0 min, S/N=10) > Is this normal? > regards > Raghavendra Gunnaiah > Ph.D. scholar > Department of Plant Science > McGill Univerisity, Canada > > > > -----Original Message----- > From: Pudney Chris (ext) GBJH [mailto:chris.pud...@syngenta.com] > Sent: Tuesday, July 10, 2012 3:24 AM > To: mzmine-devel@lists.sourceforge.net > Cc: Raghavendra Gunnaiah > Subject: Re: [Mzmine-devel] error messages > > G'day, > > > 1. I get the attached errors and window close after showing that error. > > I notice that you're using JRE 7.0 update 5. > > Could you try using JRE 6.0 update 33 instead and letting us know whether > that makes a difference please? > > Regards, > Chris. > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and delete the > original and any copies. Any use of the message by you is prohibited. > > > This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
