Hi Silvia, The program appears to be terminating as its attempting to create a temporary file to store a "raw format" version of your sequence. I wonder if there are problems writing to the /var/folders/yk/... directory, possibly due to permissions problems or a full disk. Disk space and large file problems do indeed happen more frequently with very large genomes as Joe noted, although your Lactobacillus genomes are probably quite small compared to the mammalian genomes some people are aligning.
Best, -Aaron On Fri, 2013-10-11 at 11:49 -0400, Silvia Argimon wrote: > Hello! > I started running the mauve contig mover from the command line a few > months ago. I recently changed my computer though, and it's not > working on my new system. I'm currently running Mac OS X 10.8.4, and > java version "1.6.0_51" on a 3.2 Ghz Quad-Core Intel Xeon processor. > Before I was running Mac OS X 10.6.8, and the same java version on an > iMac. > > > Here's the command and error I'm getting: > > > $ java -Xmx500m > -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar > org.gel.mauve.contig > s.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft > 8447_5__1_k90-contigs.fa > ref file: > org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align > and Reorder Contigs,normal] > shown > OS name is: Mac OS X arch: x86_64 > Executing: > progressiveMauve > --output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1 > --skip-refinement --weight=200 > --output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree > > --backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone > > /Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/LrGG.fasta > > /Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa > > Storing raw sequence > at /var/folders/yk/tqjv_9nx61n56rjpvr5v7cbc0000gn/T/rawseq10787.000 > libc++abi.dylib: terminate called throwing an exception > Exited with error code: 134 > > > I get the same error when I run this from the GUI. > > Is this because of the new OS? Should I download a new version of > Mauve? I'm running the same one as I transferred it from my old to my > new system. > Thanks you, > Silvia > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > _______________________________________________ > 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. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
