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Fix approx. lca mode

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martin-steinegger committed Dec 28, 2018
1 parent c99922e commit d16373b082cceb02b9712e7bb2074240acbaee9b
Showing with 7 additions and 2 deletions.
  1. +7 −2 data/taxonomy.sh
@@ -48,8 +48,11 @@ if [ -n "${SEARCH2_PAR}" ]; then

if [ ! -e "${TMP_PATH}/round2" ]; then
if [ -n "${APPROX_2BLCA}" ]; then
if [ ! -e "${TMP_PATH}/first_sub" ]; then
"$MMSEQS" createsubdb "${TMP_PATH}/aligned" "${TMP_PATH}/first" "${TMP_PATH}/first_sub"
fi
# shellcheck disable=SC2086
"$MMSEQS" align "${TMP_PATH}/aligned" "${TARGET}" "${TMP_PATH}/first" "${TMP_PATH}/round2" ${SEARCH2_PAR} \
$RUNNER "$MMSEQS" align "${TMP_PATH}/aligned" "${TARGET}" "${TMP_PATH}/first_sub" "${TMP_PATH}/round2" ${SEARCH2_PAR} \
|| fail "Second search died"
else
mkdir -p "${TMP_PATH}/tmp_hsp2"
@@ -96,8 +99,10 @@ if [ -n "${REMOVE_TMP}" ]; then
rm -f "${TMP_PATH}/top1" "${TMP_PATH}/top1.index"
rm -f "${TMP_PATH}/aligned" "${TMP_PATH}/aligned.index" "${TMP_PATH}/round2" "${TMP_PATH}/round2.index"
rm -f "${TMP_PATH}/merged" "${TMP_PATH}/merged.index" "${TMP_PATH}/2b_ali" "${TMP_PATH}/2b_ali.index"
if [ -n "${APPROX_2BLCA}" ]; then
rm -f "${TMP_PATH}/first_sub" "${TMP_PATH}/first_sub.index"
fi
fi

if [ -n "${LCA_PAR}" ]; then
rm -f "${TMP_PATH}/mapping" "${TMP_PATH}/mapping.index" "${TMP_PATH}/taxa" "${TMP_PATH}/taxa.index"
else

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