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- #!/bin/sh
- #$ -N velvet
- #$ -m e
- #$ -e sge_velvet.err
- #$ -o sge_velvet.out
- #$ -M adavisr@ufl.edu
- #$ -q all.q
- #$ -l mem_free=4G
- JOB_ID=$1
- PREFIX=velvet_out/$1
- mkdir -p velvet_out/
- mkdir -p $PREFIX
- for kmer in 17 31
- do
- echo "# INPUT = $1"
- echo "# OUTPUT = $PREFIX"
- echo "# L_KMER = $kmer"
- mkdir -p $PREFIX/velvet_$kmer/
- velveth $PREFIX/velvet_$kmer/ $kmer -fasta -short $1 > $PREFIX/velvet_$kmer/velveth.log
- velvetg $PREFIX/velvet_$kmer > $PREFIX/velvet_$kmer/velvetg.log
- echo "#################################################################"
- done
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