Hi ,
Can somebody point out where I am wrong in the following script for running prokka on 10 genome . A genome file which running on is named in the following manner e.g. GCA_003612255.1_ASM361225v1_AB004_genomic.fna
#specify the shell type #$ -S /bin/sh #run in the current working directory #$ -cwd #specify which queue you wish to use #$ -q amd.q #Number of threads #$ -pe multithread 2 #Limit memory #$ -l h_vmem=16G #How long it will run for (HH:MM:ss) (20 hours) #$ -l h_rt=02:00:00 #Set stack memory #$ -l h_stack=10M #Output logfile #$ -o output.log #Error logfile
-e error.log
#Make it an array #$ -t 1-10 #Run program NAME=$(head -n $SGE_TASK_ID species.txt | tail -n 1) source $HOME/.bashrc module load prokka module load barrnap prokka --outdir Myxococcus_Prokka_${NAME} --prefix ${NAME} $HOME/Myxococcus/${NAME} --cpus 2
I am assuming the nomenclature in the last line of the script is what I can't modify correctly. What would the changes be for an output of all the 10 genomes ?
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