cd %(workdir)s


[ -x %(bin)s/silent2frag.%(binext)s ] || exit 1
%(bin)s/silent2frag.%(binext)s @flags -database %(database)s -run:constant_seed -nodelay  2>&1 \
    | egrep -v 'Total' \
    | egrep -v 'Readin' \
    | egrep -v 'Cluster:' \
    | egrep -vf ../../ignore_list \
    > log

test "${PIPESTATUS[0]}" != '0' && exit 1 || true  # Check if the first executable in pipe line return error and exit with error code if so


#Make sure the contents of the results are being logged. 
cat aa3mer.1_3 >> log
cat aa9mer.1_3 >> log


