run BLASTn remotly

Question

[arfaj a]

Hello, I develop blast application and I want to send my query to NCBI server "remote". so, I develop Perl file that send a command to blastn.exe.

The command is:

$ProgramPath\\blastn.exe -task blastn -db \"$databaseName\" -query $dataPath/testinput.txt -remote -out $dataPath/testoutput.out

Where $ProgramPath=path to .exe files $databaseName = refseq_rna $dataPath = path to text files "input - output" Now, I got these error:

Error: (301.23) [CONN_Read(blast4/HTTP)]  Unable to read data: Timeout[30.000000]
Error: (301.23) [CONN_Read(blast4/HTTP)]  Unable to read data: Timeout[30.000000]
Error: NCBI C++ Exception:
    "..\..\..\..\..\src\serial\objistr.cpp", line 518: Error: byte 188696:  Frame type= eFrameClassMember, Member name= total-length ( at Blast4-reply.body.get-databases[])
Error: (311.26) SOCK#502000[1144]@130.14.29.110:80: [SOCK::Connect]  Failed pending connect(): Closed {error=10060,Operation timed out}
Error: (303.7) [URL_Connect]  Socket connect to www.ncbi.nlm.nih.gov:80 failed: Closed

Anyone can help me with this please?

Thanks,

Answer 1

[Michael]

There is a problem with your internet connection, maybe you connect to the internet through a proxy.

[arfaj a]

So ? what can I do ?

[Michael]

Check your proxy settings and internet connection.

Answer 2

[cedric.laczny]

Since previous posts posted about where the problem likely comes from, here is a post providing at least some direction to resolve the issue: Howto use NCBI programs behind a HTTP proxy

At least, that worked for me after getting the respective information, i.e., the HTTP_PROXY_HOST and HTTP_PROXY_PORT which will depend on your universities/institutes configuration.