Question: BLAST in Linux - SOCK_SetupSSL
gravatar for t.kranenburg
2.8 years ago by
t.kranenburg40 wrote:

Dear all,

After running BLAST for a while on windows, I wanted to try to make it work on Linux as well (to have some compatibility with other software). Therefore, I downloaded the linux-version of BLAST, unzipped it, and the contents look the same as for the Windows version. Therefore, I try to BLAST something:

cd Documents/ncbi-blast-2.7.1+
tblastx -db nr -query test2.fasta -remote -out test_query.txt

However, I got the following error message:

Critical: [tblastx] Secure socket layer (SSL) has not been properly initialized in the NCBI toolkit. Have you forgotten to call SOCK_SetupSSL()?

Thus, I was wondering how I should call this command in the BLAST-folder to make it work?

sock blast linux ssl • 1.2k views
ADD COMMENTlink written 2.8 years ago by t.kranenburg40

can you do tblastx -help ?

try to run something like this, given you have 2 (or at least one) fasta files with a sequence in it:

blastn -query <file1> -subject <file2>

I suspect your issue is likely related to using the remote blasting option and not directly to your local blast bin install

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by lieven.sterck9.5k

My guess is that your Linux has tblastx in $PATH, however, it's so old that it doesn't support https.

You can verify with tblastx -version

The actual tblastx of blast 2.7.1 should be in ~/Documents/ncbi-blast-2.7.1+/bin/ and thus the call would be ~/Documents/ncbi-blast-2.7.1+/bin/tblastx -db nr -query test2.fasta -remote -out test_query.txt

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by 5heikki9.2k

Or, as he entered the folder where the executable was located:

cd Documents/ncbi-blast-2.7.1+
./tblastx -db nr -query test2.fasta -remote -out test_query.txt
ADD REPLYlink written 2.8 years ago by h.mon32k

Dear all, Thank you for your comments. Indeed when I did a local BLAST (tblastx -query test2.fasta -subject test3.fasta), BLAST works. So, indeed the problem is with the -remote part of BLAST.

ADD REPLYlink written 2.7 years ago by t.kranenburg40
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