BLASTp query/options error

Question

[joana.s.pissarra]

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...

best

[GenoMax]

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.

[joana.s.pissarra]

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

Blastp, Blastx or Tblastn with word size > 5 requires a compressed alphabet lookup table 

My interpretation is that it's assuming a word_size 6 or 7 when it should be 3:

Table C3 of user manual:

option       task      type       default value    description and notes
word_size    blastp    integer    3                Word size of initial match. Valid word sizes are 2-7.

Do you know the terminal code for blast update?

Thanks a lot!

[joana.s.pissarra]

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?

[GenoMax]

Email [e-mail] and let them know.