File: spades_sc_mruber_pre.sh

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spades 3.13.1+dfsg-2
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#!/bin/bash

############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################

set -e
pushd ../../../

rm -rf /tmp/data/output/spades_output/MRUBER_PRENORM

#./spades_compile.sh
./spades.py --sc -m 160 -k 21,33,55 --12 data/input/M.ruber/prenoemalized/Mru_no9.subsample.contam.artifact.clean.fastq -o /tmp/data/output/spades_output/MRUBER_PRENORM

rm -rf ~/quast-1.3/MRUBER_PRENORM/

python3 ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER_PRENORM/ /tmp/data/output/spades_output/MRUBER_PRENORM/contigs.fasta

python3 src/test/teamcity/assess.py ~/quast-1.3/MRUBER_PRENORM/transposed_report.tsv 49100 16 2152 75.6 65 21
exitlvl=$?
popd