hmmer() function failing

[Daniel MacLean]

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

[Xinqiu Yao]

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:

> seq <- get.seq("2abl_A", outfile=tempfile())
Fetching... Please wait. Done.
> fam <- hmmer(seq, type="hmmscan", db="pfam")
* About to connect() to www.ebi.ac.uk port 443 (#1)
*   Trying 193.62.193.80...
* Connected to www.ebi.ac.uk (193.62.193.80) port 443 (#1)
...
> fam
$hit.tbl
   name        acc bias  dcl                 desc  evalue flags hindex ndom
1   SH2 PF00017.24  0.3  880           SH2 domain 5.5e-25     3  15039    2
2 SH3_1 PF00018.28  0.0 1890           SH3 domain 1.0e-13     3  15045    1
3 SH3_9  PF14604.6  0.0 2420   Variant SH3 domain 7.9e-10     3  15062    1
4 SH3_2 PF07653.17  0.0 2911   Variant SH3 domain 9.9e-09     3  15056    1
5 SH3_3 PF08239.11  1.0 3479 Bacterial SH3 domain 3.5e-06     3  15057    2
  nincluded nregions nreported    pvalue score taxid     pdb.id bitscore
1         1        2         1 -65.65455  87.3     0 PF00017.24     87.3
2         1        1         1 -39.72713  50.7     0 PF00018.28     50.7
3         1        1         1 -30.75869  38.5     0  PF14604.6     38.5
4         1        1         1 -28.22211  34.8     0 PF07653.17     34.8
5         0        2         0 -22.34951  27.2     0 PF08239.11     27.2
  mlog.evalue
1    55.85988
2    29.93361
3    20.95899
4    18.43073
5    12.56275

$url
[1] "http://www.ebi.ac.uk/Tools/hmmer/results/BA333050-5B91-11E9-8A5D-EB9BF75AEC3D"

attr(,"class")
[1] "hmmer"   "hmmscan"

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] bio3d_2.3-4.9000

loaded via a namespace (and not attached):
 [1] httr_1.3.1      compiler_3.5.1  R6_2.3.0        parallel_3.5.1
 [5] RCurl_1.95-4.11 curl_3.2        Rcpp_1.0.0      grid_3.5.1
 [9] bitops_1.0-6    XML_3.98-1.16

[Daniel MacLean]

Works great, thanks for quick help!