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Old 06-30-2011, 11:40 PM   #1
arkal
advancing one byte at a time!
 
Location: Bangalore, India

Join Date: Jun 2011
Posts: 56
Default ClustalW MPI

Hey Sorry in advance if this is a trivial doubt but i'm having trouble running Clustalw mpi.

So, i'm trying to run a multiple alignment on the sequences in the file abc.fa and generate a guide tree for it. The following is the qsub script i submit for my job. Can someone please tell me what i'm doing wrong?


#!/bin/bash
#$ -N clustalw_mpi
#$ -cwd
#$ -V
#$ -o $JOB_ID.$JOB_NAME.OUT
#$ -e $JOB_ID.$JOB_NAME.ERR
#$ -q <cluster node id>
#$ -pe mvapich2 9

/Apps/mvapich2/bin/mpiexec.hydra -np $NSLOTS -hostfile $TMPDIR/machines /Apps/denovo/clustalw-mpi-0.13/clustalw-mpi -infile=abc.fa -newtree=abc.tree


I'm running a rocks cluster v 5.3

The program ran for over 4 days (before i killed it) without generating any output in the given time.
Q1. Is there an upper limit on the number of sequences that can be handled by the program?
Q2. can anyone give me any statistics based on personal usage of the time it takes to complete its job (no of processors, number of sequences and time taken)?
Q3. Is there anything wrong with my qsub script? ( I can't seem to find any proper details on usage online)

Thanks in advance.

Last edited by arkal; 07-01-2011 at 12:07 AM.
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Old 07-03-2011, 02:25 AM   #2
colindaven
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Location: Germany

Join Date: Oct 2008
Posts: 415
Default

Why use Clustal when it has been superseded by so many other more accurate and quicker algorithms, eg muscle ?
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Old 07-03-2011, 08:55 AM   #3
arkal
advancing one byte at a time!
 
Location: Bangalore, India

Join Date: Jun 2011
Posts: 56
Default

Hmmm.... I'm a lil new to this so will check out muscle. Thanks for ur help!
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