I want to ignore certain sequences for BLAST search. It takes longer if the db is huge and I guess bigger db might inflate Hit score. My solution was to use
-entrez_query option using
nt database available in our server. But
-entrez_query option needs
-remote option and this is imcompatible with using database in the server. To get around this, I access to NCBI nt database instead of the one downloaded to our server.
Here is the code which does not work but it should work, because it works in my laptop:
nohup tblastn -query NP_040593.1.fa \ -db nt \ -remote \ -entrez_query "Viruses[ORGN] NOT (SYNTHETIC[TI] OR ENVIRONMENTAL[TI] OR PATENT[TI]) NOT (UNVERIFIED[KYWD] OR STANDARD_DRAFT[KYWD] OR VIRUS_LOW_COVERAGE[KYWD] OR VIRUS_AMBIGUITY[KYWD])" \ -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe qcovs qcovhsp' \ -out tblastn_allFiltered.out\ -export_search_strategy export.txt &> nohup.out &
When I run this exact code in our server, I get this error:
Error: NCBI C++ Exception: T0 "/home/ross/ncbi-blast-2.10.0+-src/c++/src/serial/rpcbase.cpp", line 233: Error: ncbi::CRPCClient_Base::x_Ask() - Failed to receive reply after 3 tries
I use NCBI API key which is supposeed to accept 10 request/second. I got the API key and export to ~/.bash_profile.
So, why is this not running in the cluster? Hope someone will help me here!
Thanks a million,