#!/bin/bash
#$ -S /bin/bash
#$ -N giab-8
#$ -q all.q,mpi.q
#$ -pe ncpus 12
#$ -l mem_token=3.75G,mem_free=3.75G,h_vmem=3.75G,excl=true
#$ -j y
#$ -o log/$JOB_NAME.$JOB_ID.$TASK_ID
#$ -m ae
#$ -M sjackman@gmail.com

#------------------------------------------------------------
# job params
#------------------------------------------------------------

export k=$SGE_TASK_ID
export name=hsapiens

export lib=pe600
export pe600=`<pe600.in`
export mp=mp6k
export mp6k=`<mp6k.in`

#------------------------------------------------------------
# run the assembly
#------------------------------------------------------------

export stages="unitigs contigs mp-sam scaffolds"

source /extscratch/btl/bloom-dbg/assembler-comparison/common/run-abyss-1.9.0-genesis \
	mp6k_de='--mean' mp6k_s=200 mp6k_n=1 S=100-10000 N=7 "$@"
