[Bioperl-pipeline] phylip_tree_pipeline

[Shawn Hoon]

Hi this looks like a problem with permissions.

it looks like:

     359     my $outfile =  
$self->io->catfile($self->tempdir,$self->outfile);

is not able to create the file. Check that you have correct permissions  
in your temp directory?


shawn


On Monday, December 8, 2003, at 12:58AM, Ruiz Manuel wrote:

>
>   Hi,
>
>   I'm trying to run the program phylip_tree_pipeline  with my  
> multifasta
>   file.......
>   Clustal run correctly and create a file.cls in resultdir but the  
> SeqBoot
>   program fail
>
>   ------------- EXCEPTION  -------------
>   MSG: Problems running runnableDB for
>   [
>   ------------- EXCEPTION  -------------
>   MSG: Problems running Phylip program SeqBoot:
>   ------------- EXCEPTION  -------------
>   MSG: SeqBoot did not create files correctly (/tmp/eBqU06druL/outfile)
>   STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::_run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/ 
> Phylip/Se
>  qBoot.pm:361 STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/ 
> Phylip/Se
>  qBoot.pm:311 STACK (eval)
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ 
> Phylip.
>  pm:178 STACK Bio::Pipeline::Runnable::Phylip::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ 
> Phylip.
>  pm:177 STACK Bio::Pipeline::RunnableDB::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ 
> RunnableDB.pm:35
>  1 STACK (eval)
>   /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306
>   STACK Bio::Pipeline::Job::run
>   /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304
>   STACK Bio::Pipeline::Manager::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: 
> 331
>   STACK toplevel PipelineManager:152
>
>   --------------------------------------
>
>   STACK Bio::Pipeline::Runnable::Phylip::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ 
> Phylip.
>  pm:180 STACK Bio::Pipeline::RunnableDB::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ 
> RunnableDB.pm:35
>  1 STACK (eval)
>   /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306
>   STACK Bio::Pipeline::Job::run
>   /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304
>   STACK Bio::Pipeline::Manager::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: 
> 331
>   STACK toplevel PipelineManager:152
>
>   --------------------------------------
>   ]
>
>   STACK Bio::Pipeline::Job::run
>   /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:311
>   STACK Bio::Pipeline::Manager::run
>
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: 
> 331
>   STACK toplevel PipelineManager:152
>
>   --------------------------------------
>
>   I use phylip3.5/seqboot version....It's ok?!
>
>
>
>
> -- 
> Manuel Ruiz
>
> Equipe Génomique et Bio-informatique
> CIRAD-Biotrop
> TA40/03
> Avenue Agropolis
> 34398 Montpellier Cedex 5
> France
>
> Tel : (33) 4 67 61 56 31
> Fax : (33) 4 67 61 56 05
> e-mail: manuel.ruiz at cirad.fr
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