obipr2 error -OBITools

Question

[beyariv7]

Hi,

I need to convert a PR2 database into ecoPCR database, according OBITools documentation I type:

obipr2 --local=PR2DB

but does not work

Traceback (most recent call last):
  File "/opt/OBITools-1.2.13/bin/obipr2", line 271, in <module>
    sequrl,taxurl,options.ecopcroutput = pr2URLS(options)
  File "/opt/OBITools-1.2.13/bin/obipr2", line 111, in pr2URLS
    latest = max(versions)
ValueError: max() arg is an empty sequence

I also tried with

obipr2 --localdb=PR2DB

and the same error occurs, even the next option does not work

obipr2

someone have idea of what I need to do??? Thank you!

Answer 1

[daniquijano]

I am having the same problem. Did you solve it?

According to obipr2 documentation, just executing obipr2 would recall information from an outdated website http://ssu-rrna.org/pr2/. That is weird, and is not working:

Traceback (most recent call last):
  File "/Users/daniquijano/miniconda3/bin/obipr2", line 271, in <module>
    sequrl,taxurl,options.ecopcroutput = pr2URLS(options)
  File "/Users/daniquijano/miniconda3/bin/obipr2", line 101, in pr2URLS
    archive=getHyperlink(baseurl)
  File "/Users/daniquijano/miniconda3/bin/obipr2", line 75, in getHyperlink
    furl = urllib2.urlopen(url)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 429, in open
    response = self._open(req, data)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 447, in _open
    '_open', req)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 1228, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/Users/daniquijano/miniconda3/lib/python2.7/urllib2.py", line 1198, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error [Errno 60] Operation timed out>

Therefore, I downloaded different options of PR2 database (for QIIME or Mothur, UTAX format for USEARCH and VSEARCH, and dada2 format) and saved them in a local folder. I tried to run from the parent folder:

obipr2 --localdb=PR2DB

And got the very same error as you... Anyone can help, please?