

set -ex



run_sepp.py --help
run-sepp.sh $PREFIX/share/sepp/ref/input_fragments.fasta testrun_tiny -a $PREFIX/share/sepp/ref/reference_alignment_tiny.fasta -t $PREFIX/share/sepp/ref/reference_phylogeny_tiny.nwk -r $PREFIX/share/sepp/ref/RAxML_info-reference-gg-raxml-bl.info -x 1 -b 1
grep "f__Halomonadaceae" testrun_tiny_placement.tog.relabelled.tre
grep "testseqd" testrun_tiny_placement.tog.relabelled.tre
run_upp.py --help
exit 0
