I would like to ask an information regarding SPalign. We are trying to align multiple proteins at the same time but somehow we cannot generate any output by command line: ./SP-align -qlist sdir1 qlist -tlist sdir2 tlist -odir out/ After slash I tried to insert the path of the possible output file but this error message keeps popping up "Warning, Fail to open file: out/qlist.sp", in the case of a pairing of 2 proteins the output file is not generated as well. Could you give me any hint? i would appreciate that.