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eggzilla / RNAlien

RNAlien - unsupervised RNA family model construction
http://rna.tbi.univie.ac.at/rnalien/
GNU General Public License v3.0
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HttpExceptionRequest from NCBI using command line #13

Open lcscs12345 opened 7 years ago

lcscs12345 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 5 years ago

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.