Alignment sequences with MUSCLE
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
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jr5731173 •
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The last line would be better as:
or
for file in *.faa ;would be fine if you arecding in to the directory itself.apart from the typo in muscle (not musle) it will do ok, though jrj.healey suggestion will make it more applicable
I assume this is the content of your job script? Problem with doing it this way is that
forloop 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.