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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