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/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/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
Any advice on what else I could try?
Thanks,
Silvia
On Fri, Oct 11, 2013 at 6:25 PM, Joseph Fass <joseph.f...@gmail.com> wrote:
> 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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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
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