diff --git a/data/annotatecustom.sh b/data/annotatecustom.sh index 379efa0..e902b5d 100644 --- a/data/annotatecustom.sh +++ b/data/annotatecustom.sh @@ -120,20 +120,24 @@ if notExists "${TMP_PATH}/search_not_proc.dbtype"; then #shellcheck disable=SC2086 "$MMSEQS" search "${TMP_PATH}/clu_rep" "${TARGET}" "${TMP_PATH}/search_not_proc" "${TMP_PATH}/tmp_search" ${SEARCH_PAR} --alt-ali 3 \ || fail "MMseqs2 search died" + + #shellcheck disable=SC2086 + $RUNNER "$MMSEQS" summarizeresult "${TMP_PATH}/search_not_proc" "${TMP_PATH}/searchDB" ${SUMMARIZE_PAR} \ + || fail "first sequence-profile search died" fi -if notExists "${TMP_PATH}/search_not_proc_filt.dbtype"; then +# if notExists "${TMP_PATH}/search_not_proc_filt.dbtype"; then #TODO pre-process DB here -> "${TMP_PATH}/search_not_proc_filt" #filter output - preprocessDb "${TMP_PATH}/search_not_proc" "${TMP_PATH}/search_not_proc_filt" -fi + # preprocessDb "${TMP_PATH}/search_not_proc" "${TMP_PATH}/search_not_proc_filt" +# fi #add headers if [ -n "${SIMPLE_OUTPUT}" ]; then - convertalis_simple "${TARGET}" "${TMP_PATH}/search_not_proc_filt" "${RESULTS}.tsv" + convertalis_simple "${TARGET}" "${TMP_PATH}/searchDB" "${RESULTS}.tsv" else echo "Standard output will be provided" - convertalis_standard "${TARGET}" "${TMP_PATH}/search_not_proc_filt" "${RESULTS}.tsv" + convertalis_standard "${TARGET}" "${TMP_PATH}/searchDB" "${RESULTS}.tsv" fi #remove temporary files and directories