Hi Tom, Thank you for your comments. I do have a MacPro with 4Gb of RAM and could align about 15 bacterial genomes... but I do it from a .gb file that was provided by the bioinformatician (what I am not ). ... Of course it took long time... about 20 hours to finish the job, and I should stop doing most of other tasks.
Regards Cristina ----- Original Message ----- > From: Tom Geissmann <tom.geissm...@inserm.fr> > To: mauve-users@lists.sourceforge.net > Date: 2015-01-23 22:27:00 > Subject: Re: [Mauve-users] Mauve downloading problems in MacOX Yosemite + > Windows Exited error code:3 > > Hi, > I’ve some commentaries: > > > > > you will need a machine with 32 or 64GB of RAM. If you've got draft > > I aligned successfully 42 bacterial genomes (S. aureus) from the same > genotype, if I use different genotypes, I can align about 15 genomes with a > MacPro with 32 GB of RAM > > > genomes, reordering the contigs relative to a single reference will help > > reduce memory demands for the subsequent multiple alignment. > > for me it’s not the case: progmauve works better with unordered genomes for > me! (What it is really not logic for me, Aaron, I think that I have send you > my genomes) > > All the best, > > Tom > > > > > As for the problem on windows, would you be able to send a bit more of > > the text preceding the exit error message? It would help to know what > > the aligner was doing right before it crashed. Best to send the whole > > log if possible, although if it's big then maybe better to email it to > > me off-list. > > > > Cheers, > > -Aaron > > > > > > On Thu, 2015-01-22 at 16:33 +1100, cav00004 wrote: > >> Dear Aaron, > >> > >> Thank you for your quick reply. > >> I simply downloaded the new version v2.4.0 and it seems to work properly. > >> I lunched yesterday an alignment of 16 bacterial g > >> enomes, about 3Gb each, and is still working... so is great. I think now > >> the only limitation is the RAM memory as I use my p > >> ersonal computer and is not very performant: > >> > >> - MacBook Pro (13 inch, late 2011) > >> - Processor 2,4 GHz Inter Core i5 > >> - Memory 4 Go 1333 MHz DDR3 > >> - Graphics Inter HD Graphics 3000 384 Mo > >> > >> I will need to add another 19 sequences to the alignment, so a total of 35 > >> bacterial genomes. Do you think I will have any t > >> rouble? Will Mauve have difficulties to align such a big number of > >> sequences? > >> > >> In the other hand, I was intended to work with the PC at the laboratory, a > >> common PC, and I had no problem recently, but sud > >> denly it appeared an error message after just lunching the alignment. I > >> downloaded the new version as well for Windows, but > >> the problem was not solved. The error message is the following: > >> > >> Error: mauve Aligner exited with and error code. Check the log window > >> for details. > >> > >> When checking the log window (Mauve Console?), the last line says: > >> "This application has requested the Runtime to terminate it in an > >> unusual way. > >> Please contact the application's support team for more information. > >> Exited with error code: 3" > >> > >> Please, can you help me to solve the problem with the Windows version? > >> > >> Thank you very much in advance > >> > >> Cristina > >> > >> > >> ------------------------ > >> Cristina Andres-Barrao, PhD. > >> cav00...@nodai.ac.jp > >> Laboratory of Fermentation Biochemistry > >> Department of Fermentation Sciences > >> Faculty of Applied Biosciences > >> Tokyo University of Agriculture > >> 1-1-1 Sakuragaoka, Setagaya-ku > >> Tokyo 156-8502, Japan > >> > >> ------------------------------------------------------------------------------ > >> New Year. New Location. New Benefits. New Data Center in Ashburn, VA. > >> GigeNET is offering a free month of service with a new server in Ashburn. > >> Choose from 2 high performing configs, both with 100TB of bandwidth. > >> Higher redundancy.Lower latency.Increased capacity.Completely compliant. > >> http://p.sf.net/sfu/gigenet > >> _______________________________________________ > >> Mauve-users mailing list > >> Mauve-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/mauve-users > > > > -- > > Aaron E. Darling, Ph.D. > > Associate Professor, ithree institute > > University of Technology Sydney > > Australia > > > > http://darlinglab.org > > twitter: @koadman > > > > > > > > > > > > UTS CRICOS Provider Code: 00099F > > DISCLAIMER: This email message and any accompanying attachments may contain > > confidential information. > > If you are not the intended recipient, do not read, use, disseminate, > > distribute or copy this message or > > attachments. If you have received this message in error, please notify the > > sender immediately and delete > > this message. Any views expressed in this message are those of the > > individual sender, except where the > > sender expressly, and with authority, states them to be the views of the > > University of Technology Sydney. > > Before opening any attachments, please check them for viruses and defects. > > > > Think. Green. Do. > > > > Please consider the environment before printing this email. > > ------------------------------------------------------------------------------ > > New Year. New Location. New Benefits. New Data Center in Ashburn, VA. > > GigeNET is offering a free month of service with a new server in Ashburn. > > Choose from 2 high performing configs, both with 100TB of bandwidth. > > Higher redundancy.Lower latency.Increased capacity.Completely compliant. > > http://p.sf.net/sfu/gigenet > > _______________________________________________ > > Mauve-users mailing list > > Mauve-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > ------------------------------------------------------------------------------ > New Year. New Location. New Benefits. New Data Center in Ashburn, VA. > GigeNET is offering a free month of service with a new server in Ashburn. > Choose from 2 high performing configs, both with 100TB of bandwidth. > Higher redundancy.Lower latency.Increased capacity.Completely compliant. > http://p.sf.net/sfu/gigenet > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------ Cristina Andres-Barrao, PhD. cav00...@nodai.ac.jp Laboratory of Fermentation Biochemistry Department of Fermentation Sciences Faculty of Applied Biosciences Tokyo University of Agriculture 1-1-1 Sakuragaoka, Setagaya-ku Tokyo 156-8502, Japan ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
