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Hi all!

I need to convert PR2 database to ecoPCR format. I made a dir called PR2Dir and ran this command from its parent folder, following obipr2 instructions:

obipr2

It didn't work:

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>

In fact, the obipr2 instructions state that the above mentioned command would download the database from a deprecated version of PR2 website: http://ssu-rrna.org/pr2/

Therefore, I tried to directly download it from the new website (https://pr2-database.org/documentation/pr2-files/) and use obipr2 locally. I tried all the possible combinations with these 2 commands:

obipr2 --local=PR2Dir

And: obipr2 --localdb=PR2Dir

And all the possible formats of PR2 database downloadable from the mentioned web site (two file format for Mothur and QIIME, dada2 format, UTAX format for USEARCH and VSEARCH, and taxo_long for BLAST). I tried placing these files either in the PRDir2 folder or in its parent folder. In all the mentioned combinations I got this error:

File "/Users/daniquijano/miniconda3/bin/obipr2", line 271, in <module>
    sequrl,taxurl,options.ecopcroutput = pr2URLS(options)
  File "/Users/daniquijano/miniconda3/bin/obipr2", line 111, in pr2URLS
    latest = max(versions)
ValueError: max() arg is an empty sequence

Is there a way to fix or bypass that? Maybe using a particular format from the ones available at PR2, then editing it (using sed, obiannotate and others??) and finally using obiconvert to turn fasta file into ecoPCR database? But how should the fasta file that was to be converted to ecoPCR database look like?

Thank you for your attention!