Alignment sequences with MUSCLE

Question

[jr5731173]

Hello, I want to do multiple sequences alingment in all files contained in a directory, all of them with .faa extension, I want to run the muscle software in a PBS script I don't know if the next command line is correct

#PBS -N muscle_core
#PBS -l nodes=1:ppn=16,mem=16gb,vmem=32gb,walltime=250:00:00
#PBS -q default
#PBS -V

cd $PBS_O_WORKDIR

module load muscle/3.8.31

for file in $*.faa; do musle -in $file -out "${file}_aln.faa; done

My data are in /LUSTRE/user/username

[Joe]

The last line would be better as:

for file in /path/to/dir/*.faa ; do muscle -in "$file" -out "${file%.*}"_aln.faa ; done

or for file in *.faa ; would be fine if you are cding in to the directory itself.

[lieven.sterck]

apart from the typo in muscle (not musle) it will do ok, though jrj.healey suggestion will make it more applicable

[GenoMax]

I assume this is the content of your job script? Problem with doing it this way is that for loop executes under a single PBS job (unless you do job arrays, an example here).

Otherwise you would want to use something like this to submit multiple jobs at the same time.