Hi Silvia, After thinking about this for a while I am beginning to suspect there may be a problem with the input files. Would it be possible for you to send me the input files off-list either via compressed e-mail attachment or dropbox so I can test it?
Thanks, -Aaron On Mon, 2013-10-14 at 12:49 -0400, Silvia Argimon wrote: > Dear Joseph and Aaron, > Thank you for your messages. As Aaron mentioned my genomes are small > (2-4 Mb) so that shouldn't be a problem (it certainly hasn't been a > problem in the past). > I had a look at the /var/folders/yk/ directory and the permissions > appeared as rwxr-xr-x. To address potential permissions issues, I > chmod 777 the directory and the temp folder > "tqjv_9nx61n56rjpvr5v7cbc0000gn" in it, and all the subdirectories in > that too. Then tried again, but got the same error. > I also tried to run the same command with sudo, but again same error. > > > $ java -Xmx500m > -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar > org.gel.mauve.contigs.ContigOrderer -output batch 1_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/ali gnment1/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/rawseq813.000 libc++abi.dylib: terminate called throwing an exception Exited with error code: 134 > > > > I also tried to run the same command with sudo, but again same error, > though the raw sequenced seemed to have been directed to another > location in this case. > > $ sudo java -Xmx500m > -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.ja r > org.gel.mauve.contigs.ContigOrderer -output batch1_assembly_1_mcm -ref > LrGG.fasta -draft 8447_5__1_k90-contigs.fa Password: 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 /tmp/rawseq773.000 libc++abi.dylib: terminate called throwing an exception Exited with error code: 134 -- 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. ------------------------------------------------------------------------------ Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
