hmmer() function failing
Below code (from example) fails
seq <- get.seq("2abl_A", outfile=tempfile()) fam <- hmmer(seq, type="hmmscan", db="pfam")
Error in resurl["uuid", 1] : incorrect number of dimensions
fails with other sequences I've tried. Verbose output:
- Trying 193.62.193.80...
- TCP_NODELAY set
-
Connected to www.ebi.ac.uk (193.62.193.80) port 80 (#0)
POST /Tools/hmmer/search/hmmscan HTTP/1.1 Host: www.ebi.ac.uk Accept:text/xml Content-Length: 185 Content-Type: application/x-www-form-urlencoded
-
upload completely sent off: 185 out of 185 bytes < HTTP/1.1 301 Moved Permanently < Content-Type: text/html < Date: Tue, 09 Apr 2019 10:32:34 GMT < Location: https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan < Connection: Keep-Alive < Content-Length: 0 <
- Connection #0 to host www.ebi.ac.uk left intact
- Issue another request to this URL: 'https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan'
- Switch from POST to GET
- Trying 193.62.193.80...
- TCP_NODELAY set
- Connected to www.ebi.ac.uk (193.62.193.80) port 443 (
#1) - ALPN, offering http/1.1
- Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
- successfully set certificate verify locations:
- CAfile: /etc/ssl/cert.pem CApath: none
- SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
- ALPN, server accepted to use http/1.1
- Server certificate:
- subject: jurisdictionCountryName=GB; businessCategory=Government Entity; serialNumber=Government Entity; C=GB; ST=Cambridgeshire; L=CAMBRIDGE; O=European Bioinformatics Institute; OU=European Bioinformatics Institute; CN=www.ebi.ac.uk
- start date: May 10 11:41:12 2018 GMT
- expire date: May 10 11:51:00 2020 GMT
- subjectAltName: host "www.ebi.ac.uk" matched cert's "www.ebi.ac.uk"
- issuer: C=BM; O=QuoVadis Limited; CN=QuoVadis EV SSL ICA G3
- SSL certificate verify ok.
GET /Tools/hmmer/search/hmmscan HTTP/1.1 Host: www.ebi.ac.uk Accept:text/xml
< HTTP/1.1 200 OK
< Server: Apache/2.2.15 (Red Hat)
< Vary: Content-Type
< Cache-Control: max-age=0
< Content-Type: text/xml
< Strict-Transport-Security: max-age=0
< Date: Tue, 09 Apr 2019 10:32:35 GMT
< Access-Control-Max-Age: 1000
< Expires: Tue, 09 Apr 2019 10:32:35 GMT
< Access-Control-Allow-Origin: *
< Connection: Keep-Alive
< Set-Cookie: hmmerserver_session=f4348259d0fc0428a306f02280004f38db24a22e; path=/; expires=Wed, 17-Apr-2019 10:32:35 GMT; HttpOnly
< Access-Control-Allow-Methods: HEAD, POST, GET, OPTIONS, DELETE, PUT
< Access-Control-Allow-Headers: x-requested-with, Content-Type, origin, authorization, accept, client-security-token
< Content-Length: 84
<
* Connection #1 to host www.ebi.ac.uk left intact
Error in resurl["uuid", 1] : incorrect number of dimensions
SessionInfo() in attachment
Comments (3)
-
-
reporter Works great, thanks for quick help!
-
reporter - changed status to closed
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Can you upgrade your bio3d to the latest development version? (See https://bitbucket.org/Grantlab/bio3d/wiki/How%20to%20download%20and%20install%20the%20development%20version for more detail)? With it, you should have no error: