## number of slots needs to be one or divisible by three
        SLOTS=\${GALAXY_SLOTS:-1};
        while [ \$SLOTS -gt 1 ]; 
        do
            if ! (( \$SLOTS % 3 )) ; then break; fi; 
            ((SLOTS--));
        done;
        if [[ "\${GALAXY_SLOTS:-1}" -ne "\$SLOTS" ]]; then
            >&2 echo "Warning: using only \$SLOTS threads (instead of the configured \${GALAXY_SLOTS:-1}), since it needs to be 1 or a multiple of three. Please contact your Galaxy Admin";
        fi;

        kc-align
            --mode '$position.mode'
            --reference '$ref'
            --sequences '$seqs'
            #if $position.mode == "genome":
                --start '$position.start'
                --end '$position.end'
                -d '$position.dist'
            #end if
            #if $position.mode == "mixed":
                -d '$position.dist'
            #end if
            $compress
            -th "\$SLOTS"