olivier sallou <olivier.sal...@gmail.com> writes: >> I guess that's due to the new version of ncbi-tools+. Any suggested >> patch for this problem? >> > By the way, adding dbtype with prot or nuc value should do the job. > If dataset_201401/MFO/goasp.fasta contains only acgtn chars it is nuc > If it contains other letters it is prot
The input files definitely look like protein data, as confirmed by the output filenames (*.fasta.p??). However, metastudent-data's makefile can't pass -dbtype prot directly unless it starts running makeblastdb directly; as it is, it should add "-p". (FTR, for nucleotides, the option would be "-p F".) An equivalent makeblastdb command line would take the form makeblastdb -in .../goasp.fasta -dbtype prot -out .../goasp.fasta I would also recommend updating metastudent-data's build dependency on blast2 to either ncbi-blast+ or ncbi-blast+-legacy (>= 2.5) | blast2 depending on whether it winds up running makeblastdb directly or via formatdb. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
