HttpExceptionRequest from NCBI using command line

[lcscs12345]

Hi,

For of all thank you making this useful tools available. However, I received the following error when using the command line version.

$ RNAlien -i snRNA.fa -t 1396 -c 20
RNAlien-bin: HttpExceptionRequest Request {
host = "www.ncbi.nlm.nih.gov"
port = 443
secure = True
requestHeaders = []
path = "/"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
}
(InternalException (HandshakeFailed (Error_Protocol ("certificate has unknown CA",True,UnknownCa))))

[eggzilla]

Hey, thanks for reporting the error and using RNAlien! I have a other users also reporting this error.
Have you just installed the tool and the error appeared in the first attempt to use it, or did it work before?
Which operating system/linux distribution are you using?

[lcscs12345]

This is the first attempt. I tried it on Red Hat Enterprise Linux Server release 7.3 (Maipo) and CentOS Linux release 7.3.1611 (Core) on different networks. I installed RNAlien using conda.

[eggzilla]

Hey, the other affected user is also on Red Hat Enterprise Linux. I think that the required Root certificate that covers NCBI is not installed by default by RHEL. Could you give the following guide a try? I guess it could also be helpful to you in other instances:
https://techjourney.net/update-add-ca-certificates-bundle-in-redhat-centos/
I will also try to deactivate the certificate check in the library, but it might take some time :-)

[eggzilla]

Hi, if you use the installation via bioconda the problem should be resolved. There is also a new offline mode in RNAlien version 1.6.0, which does not rely on remote connections for blast and sequence retrieval anymore.