I am performing standalone blastp, I already used these commands on windows but I am having trouble in Linux with the same blast version (2.2.30+)
My cmd line:
blastp -task blastp -import_search_strategy 31U1MWCX015_search_strategy.asn -query uniprot-yourlist.fasta -db testdb -outfmt "6 qseqid qlen qseq sseqid length qstart qend evalue bitscore pident nident ppos positive" -out blastpoistocheck Warning: Overriding database/subject in saved strategy Warning: Overriding query in saved strategy **BLAST query/options error: Blastp, Blastx or Tblastn with word size > 5 requires a compressed alphabet lookup table** Please refer to the BLAST+ user manual.
my testdb is good / my import strategy appears to be working / the problem is really with the query
I already tried many query files - .txt, .fa and this one is downloaded directly from uniprot compressed and extracted in the same folder as .fasta
I tried specifying the -word_size 3 and it doesn't work
I don't really know what they mean by "compressed alphabet" (my txt files are UTF-8 and I also tried Western ISO-8859-15 + windowsline ending) and BLAST+ user manual doesn't really help.
I ran out of troubleshooting ideas ... I really hope you can help me with this one - I couldn't find threads adressing this issue...