Add --gpu to databases

Author: martin-steinegger

data/workflow/databases.sh

@@ -306,15 +306,15 @@ case "${INPUT_TYPE}" in
     "FASTA_LIST")
         eval "set -- $ARR"
         # shellcheck disable=SC2086
-        "${MMSEQS}" createdb "${@}" "${OUTDB}" ${COMP_PAR} \
+        "${MMSEQS}" createdb "${@}" "${OUTDB}" ${COMP_PAR} --gpu 1 \
             || fail "createdb died"
         for i in "${@}"; do
             rm -f -- "$i"
         done
     ;;
     "FSA")
         # shellcheck disable=SC2086
-        "${MMSEQS}" createdb "${TMP_PATH}/"*.fsa "${OUTDB}" ${COMP_PAR} \
+        "${MMSEQS}" createdb "${TMP_PATH}/"*.fsa "${OUTDB}" ${COMP_PAR} --gpu 1 \
             || fail "createdb died"
         rm -f -- "${TMP_PATH}/"*.fsa
     ;;
@@ -385,7 +385,7 @@ case "${INPUT_TYPE}" in
         sed 's|_protein\.faa\.gz||g' "${TMP_PATH}/tardb.lookup" > "${TMP_PATH}/tardb.lookup.tmp"
         mv -f -- "${TMP_PATH}/tardb.lookup.tmp" "${TMP_PATH}/tardb.lookup"
         # shellcheck disable=SC2086
-        "${MMSEQS}" createdb "${TMP_PATH}/tardb" "${OUTDB}" ${COMP_PAR} \
+        "${MMSEQS}" createdb "${TMP_PATH}/tardb" "${OUTDB}" ${COMP_PAR} --gpu 1 \
             || fail "createdb died"
         if [ -n "${REMOVE_TMP}" ]; then
             # shellcheck disable=SC2086

src/util/createdb.cpp

@@ -52,9 +52,6 @@ int sortWithIndex(const char *dataFileSeq,
     setvbuf(seqOut, NULL, _IOFBF, 1024*1024*50);
     size_t offset = 0;
     for (size_t i = 0; i < reader.getSize(); i++) {
-        if(index[i].length == 28){
-            std::cout << "Warning: Sequence with length 28 found in " << dataFileSeq << ". This is likely a bug in the database creation.\n";
-        }
         size_t written = fwrite(buf + index[i].offset, 1, index[i].length, seqOut);
         if (written != static_cast<size_t>(index[i].length)) {
             Debug(Debug::ERROR) << "Can not write to data file " << dataFileSeq << "\n";