[Bioperl-l] Trouble about Bio::Tools::Run::Alignment::Clustalw

click xu click.xu at gmail.com
Tue Mar 30 00:03:49 EDT 2010


Russell
Clustalw2 can correctly run in command line, and the /tmp space is enough too.


2010/3/30 Smithies, Russell <Russell.Smithies at agresearch.co.nz>:
> Do you have enough temp space?
> Will clustalw run 'manually' with your parameters from the command line?
>
> --Russell
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of click xu
>> Sent: Tuesday, 30 March 2010 4:17 p.m.
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Trouble about Bio::Tools::Run::Alignment::Clustalw
>>
>> Hi,
>> I meet a problem when using Clustalw module.
>> Here is the error message:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: ClustalW call ( align  -infile=/tmp/AeyAfdxGvH/YpcPbyhYht
>> -output=gcg   -matrix=BLOSUM -ktup
>> le=2 -outfile=/tmp/AeyAfdxGvH/Z2MbO0ylbF 2>&1) failed to start: 0 |
>> cannot find the file or path
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /home/lf/data/BioPerl-
>> 1.6.1/Bio/Root/Root.pm:368
>> STACK: Bio::Tools::Run::Alignment::Clustalw::_run
>> /usr/local/share/perl/5.10.0/Bio/Tools/Run/Alig
>> nment/Clustalw.pm:756
>> STACK: Bio::Tools::Run::Alignment::Clustalw::align
>> /usr/local/share/perl/5.10.0/Bio/Tools/Run/Ali
>> gnment/Clustalw.pm:515
>> STACK: test.txt:45
>> -----------------------------------------------------------
>> The test program is described as below:
>> -----------------------------------------------------------
>> @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
>> $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
>> # @seq_array is an array of Bio::Seq objects
>> $aln = $factory->align(\@seq_array);
>> -----------------------------------------------------------
>> The work path of clustalw2 has been configured:
>> export CLUSTALDIR=/usr/local/bin/clustalw2
>> So, what may be reason of the error?
>> Thanks!
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>



More information about the Bioperl-l mailing list