1#!/bin/sh -e 2fail() { 3 echo "Error: $1" 4 exit 1 5} 6 7notExists() { 8 [ ! -f "$1" ] 9} 10 11if notExists "${TMP_PATH}/query.dbtype"; then 12 # shellcheck disable=SC2086 13 "$MMSEQS" createdb "$@" "${TMP_PATH}/query" ${CREATEDB_QUERY_PAR} \ 14 || fail "query createdb died" 15fi 16 17if notExists "${TMP_PATH}/result.dbtype"; then 18 # shellcheck disable=SC2086 19 "$MMSEQS" taxonomy "${TMP_PATH}/query" "${TARGET}" "${TMP_PATH}/result" "${TMP_PATH}/taxonomy_tmp" ${TAXONOMY_PAR} \ 20 || fail "Search died" 21fi 22 23if notExists "${RESULTS}_lca.tsv"; then 24 # shellcheck disable=SC2086 25 "$MMSEQS" createtsv "${TMP_PATH}/query" "${TMP_PATH}/result" "${RESULTS}_lca.tsv" ${CREATETSV_PAR} \ 26 || fail "createtsv died" 27fi 28 29# shellcheck disable=SC2086 30"$MMSEQS" taxonomyreport "${TARGET}" "${TMP_PATH}/result" "${RESULTS}_report" ${TAXONOMYREPORT_PAR} \ 31 || fail "taxonomyreport died" 32 33#if notExists "${TMP_PATH}/result_aln.dbtype"; then 34# # shellcheck disable=SC2086 35# "$MMSEQS" filterdb "${TMP_PATH}/result" "${TMP_PATH}/result_aln" --extract-lines 1 ${THREADS_COMP_PAR} \ 36# || fail "filterdb died" 37#fi 38 39if notExists "${TMP_PATH}/result_aln_swapped.dbtype"; then 40 # shellcheck disable=SC2086 41 "$MMSEQS" swapresults "${TMP_PATH}/query" "${TARGET}" "${TMP_PATH}/result_aln" "${TMP_PATH}/result_aln_swapped" ${SWAPRESULT_PAR} \ 42 || fail "filterdb died" 43fi 44 45if notExists "${TMP_PATH}/result_aln_swapped_sum.dbtype"; then 46 # shellcheck disable=SC2086 47 "$MMSEQS" summarizealis "${TMP_PATH}/result_aln_swapped" "${TMP_PATH}/result_aln_swapped_sum" ${THREADS_COMP_PAR} \ 48 || fail "filterdb died" 49fi 50 51if notExists "${TMP_PATH}/result_aln_swapped_sum_tax.dbtype"; then 52 # shellcheck disable=SC2086 53 "$MMSEQS" addtaxonomy "${TARGET}" "${TMP_PATH}/result_aln_swapped_sum" "${TMP_PATH}/result_aln_swapped_sum_tax" ${ADDTAXONOMY_PAR} \ 54 || fail "filterdb died" 55fi 56 57# shellcheck disable=SC2086 58"$MMSEQS" createtsv "${TARGET}" "${TMP_PATH}/result_aln_swapped_sum_tax" "${RESULTS}_tophit_report" ${CREATETSV_PAR} \ 59 || fail "filterdb died" 60 61# shellcheck disable=SC2086 62"$MMSEQS" convertalis "${TMP_PATH}/query" "${TARGET}" "${TMP_PATH}/result_aln" "${RESULTS}_tophit_aln" ${CONVERT_PAR} \ 63 || fail "convertalis died" 64 65if [ -n "${REMOVE_TMP}" ]; then 66 # shellcheck disable=SC2086 67 "$MMSEQS" rmdb "${TMP_PATH}/result" ${VERBOSITY} 68 if [ -z "${LEAVE_INPUT}" ]; then 69 # shellcheck disable=SC2086 70 "$MMSEQS" rmdb "${TMP_PATH}/query" ${VERBOSITY} 71 # shellcheck disable=SC2086 72 "$MMSEQS" rmdb "${TMP_PATH}/query_h" ${VERBOSITY} 73 fi 74 # shellcheck disable=SC2086 75 "$MMSEQS" rmdb "${TMP_PATH}/result_aln" ${VERBOSITY} 76 # shellcheck disable=SC2086 77 "$MMSEQS" rmdb "${TMP_PATH}/result_aln_swapped" ${VERBOSITY} 78 # shellcheck disable=SC2086 79 "$MMSEQS" rmdb "${TMP_PATH}/result_aln_swapped_sum" ${VERBOSITY} 80 # shellcheck disable=SC2086 81 "$MMSEQS" rmdb "${TMP_PATH}/result_aln_swapped_sum_tax" ${VERBOSITY} 82 83 rm -rf "${TMP_PATH}/taxonomy_tmp" 84 rm -f "${TMP_PATH}/easytaxonomy.sh" 85fi 86