"Expectation Failed" error when attempting a hmmsearch with hmmer command

[Federico Olivieri]

When attempting a hmmsearch or jackhmmer with the Hmmer command, I get a "Expectation Failed" error but I do not get it when attempting the same command against "phmmer" or "hmmscan"

This was done as part of the Ensemble NMA part 2 tutorial. The previous steps where done as detailed in the tutorial.

seq <- get.seq("1rx2_A")
pfam <- hmmer(seq, type="hmmscan", db="pfam")
pfam$hit.tbl
pfam.aln <- pfam(pfam$hit.tbl$acc[1])
print(pfam.aln, alignment=FALSE)
hmm <- hmmer(pfam.aln, type="hmmsearch", db="pdb")

Error:

> hmm <- hmmer(pfam.aln, type="hmmsearch", db="pdb")
* Hostname was NOT found in DNS cache
*   Trying 157.92.32.86...
* Connected to proxy.fcen.uba.ar (157.92.32.86) port 8080 (#28)
> POST http://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch HTTP/1.1
Host: www.ebi.ac.uk
Proxy-Connection: Keep-Alive
Accept:text/xml
Content-Length: 82206
Content-Type: application/x-www-form-urlencoded
Expect: 100-continue

< HTTP/1.1 417 Expectation Failed
* Server squid/2.7.STABLE9 is not blacklisted
< Server: squid/2.7.STABLE9
< Date: Tue, 28 Mar 2017 21:35:41 GMT
< Content-Type: text/html
< Content-Length: 2315
< X-Squid-Error: ERR_INVALID_REQ 0
< X-Cache: MISS from proxy.uba.ar/1
< X-Cache-Lookup: NONE from proxy.uba.ar/1:8080
< X-Cache: MISS from proxy4.fcen.uba.ar
< X-Cache-Lookup: MISS from proxy4.fcen.uba.ar:8080
< Via: 1.0 proxy1.gestion.uba.ar:8080 (squid/2.7.STABLE9), 1.1 proxy4.fcen.uba.ar (squid/3.4.8)
< Connection: keep-alive
* HTTP error before end of send, stop sending
< 
* Closing connection 28
Error: Expectation Failed

[Lars Skjærven]

Thanks for reporting.

These function calls look fine this morning (see exception below). Note that these functions are relying on online resources. If e.g. the hmmer server does not reply as expected you'll see various types of errors.

Alternative function calls that might help in case certain servers are down:

# sequence from PDB
pdb <- read.pdb("1rx2")
pdb <- trim(pdb, chain="A")
aa <- pdbseq(pdb)

# sequence from uniprot
uni <- uniprot("DYR_ECOLI")
aa <- uni$sequence

# blast instead of hmmer
blast <- blast.pdb(aa)

Note: A previous version of Bio3d gave an error with function get.seq. Make sure you have bio3d_2.3-1 installed.

> seq <- get.seq("1rx2")  

Download failed. Re-trying URL:
  http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&val=1rx2&report=fasta&retmode=text