Hello everyone,
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...
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joana.s.pissarra •
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Cross-reference with PDB database
written by adirsommer •
Keith Bradnam had found this last year. Based on the notes there your valid options are 6 or 7.
If you are able to update blast to 2.3.0 then give that a try and see if if that fixes this.
It was one of the first pages I found :)
I tried changing the word_size for the search (3/6/7) and it doesn't work.. I don't see any other suggestions to solve it.
It's telling me
My interpretation is that it's assuming a
word_size6 or 7 when it should be 3:Table C3 of user manual:
Do you know the terminal code for blast update?
Thanks a lot!
Ok, currently working with blast-2.3.0+-src and it returns the same error:
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.
not sure what to try next... is it really a bug?
Email blast-help@ncbi.nlm.nih.gov and let them know.