News: Blastn remote times out, resolved in version 2.12.0
Just sharing my experience in the hope it will be helpful to someone...
I was frustrated when running blastn 2.6.0 using the -remote option as a result of getting this error response on multiple Ubuntu machines:
Error: NCBI C++ Exception: T0 "/build/ncbi-blast+-GcQwD4/ncbi-blast+-2.6.0/c++/src/serial/rpcbase.cpp", line 244: Error: ncbi::CRPCClient_Base::x_Ask() - Failed to receive reply after 3 tries
A Biostars post indicated 2.7.1 works, but I got the same result when I tried that. Then I upgraded to the lastest blastn, version 2.12.0, and it worked! Hopefully consistently.
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While this is useful to know
v.2.6is 5 years old.blast+introduced a new format for blast databases (v.5) withblast+ v.2.8.1. This may have been the main problem why you were getting those errors.