That same error code has appeared previously on this list for (at least in
one case) alignment of large - e.g. mammalian - genomes. Are you ordering
something large?
~Joe
On Fri, Oct 11, 2013 at 8:49 AM, Silvia Argimon <s...@nyu.edu> 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
>
>
>
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>
--
Joseph Fass
Lead Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
jnf...@ucdavis.edu
phone ~ 530.752.2698
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