Obisilva (obitools) not working

Question

[jade.ezzedine]

Hello, I need some help with Obisilva command from obitools.

My PC environment is Ubuntu 16.04 LTS.

I work on 16S rDNA. I have data sequenced with Illumina Hiseq technology.

I used obitools for Merging, Demultiplexing, Filtering, but I used vsearch to detect chimera and Swarm for clustering.

Then I want it to create a database with ecoPCR from obitools for taxonomic assignment with ecoTag. I want absolutely to use arb-SILVA database instead of NCBI, hence the usage of obisilva command to format this database into ecoPCR format. Unfortunately, unlike all previous steps, this one is not going smoothly at all.

When I type in my terminal :

 obisilva --ssu --parc

or even when I type --ssu --ref or --lsu --parc or --lsu --ref ; I get this error:

root@coldsunshine-Precision-Tower-7910:/home/coldsunshine/Desktop# obisilva --ssu --parc

Traceback (most recent call last):

  File "/usr/local/bin/obisilva", line 319, in <module>
    sequrl,taxurl,options.ecopcroutput = silvaURLS(options)

  File "/usr/local/bin/obisilva", line 151, in silvaURLS
    taxonomy=getHyperlink(baseurl+"/taxonomy")

  File "/usr/local/bin/obisilva", line 124, in getHyperlink
    furl = urllib2.urlopen(url)

  File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)

  File "/usr/lib/python2.7/urllib2.py", line 435, in open
    response = meth(req, response)

  File "/usr/lib/python2.7/urllib2.py", line 548, in http_response
    'http', request, response, code, msg, hdrs)

  File "/usr/lib/python2.7/urllib2.py", line 467, in error
    result = self._call_chain(*args)

  File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)

  File "/usr/lib/python2.7/urllib2.py", line 654, in http_error_302
    return self.parent.open(new, timeout=req.timeout)

  File "/usr/lib/python2.7/urllib2.py", line 435, in open
    response = meth(req, response)

  File "/usr/lib/python2.7/urllib2.py", line 548, in http_response
    'http', request, response, code, msg, hdrs)

  File "/usr/lib/python2.7/urllib2.py", line 473, in error
    return self._call_chain(*args)

  File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)

  File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)

urllib2.HTTPError: HTTP Error 404: Not Found

Then I saw that I can manually download the arb-SILVA database along the taxonomy. Therefore I downloaded : "SILVA_132_SSUParc_tax_silva.fasta" and "tax_slv_ssu_128.txt. I stored both files in a folder named ObiSilva. Then I tried the obisilva local option:

obisilva --ssu --parc --local=/home/coldsunshine/Desktop/ObiSilva

But I am getting another error message no matter what combination I tried

root@coldsunshine-Precision-Tower-7910:/home/coldsunshine/Desktop# obisilva --ssu --parc --local=/home/coldsunshine/Desktop/ObiSilva

Traceback (most recent call last):

  File "/usr/local/bin/obisilva", line 319, in <module>
sequrl,taxurl,options.ecopcroutput = silvaURLS(options)

  File "/usr/local/bin/obisilva", line 147, in silvaURLS
    taxonomy= dict((f,"taxonomy/"+f) for f in listdir(options.local+'/taxonomy') if isfile(join(options.local+'/taxonomy',f)))

OSError: [Errno 2] No such file or directory: '/home/coldsunshine/Desktop/ObiSilva/taxonomy'

Please help me, I am stuck at this step. Am I doing something wrong? or maybe because the arb-SILVA changed something in their website? I tried to look into obisilva script : obisilva.py but I am not that good in programming. The url seems the one and the file name also. Or I am missed something?

Thank you very much in advance for your help

[vimalkvn]

With obitools version 1.2.11, the obisilva --ssu --parc command works fine. You should try again after updating obitools if you have an older version.

[jade.ezzedine]

Thank you very much, it did work after updating. I didn't think about updating since the first time I installed obitools it took me so much time to make it work on ubuntu 16. Thanks again for your answer.

[jade.ezzedine]

Hello again, I really need some help. I asked both author to patch their script but no answer. I looked into arb-silva and I saw they changed the release location. Plus the 132 release doesn't contain tax_slv_ssu. Only the 128 release containn tax_slv_ssu and the format is in diff and not txt. So from there I tried to look into obisilva code and changed this:

siteurl="http://www.arb-silva.de/"

baseurl="%sno_cache/download/archive/release_128/Exports/" % siteurl

# (options.rrna,options.nr)

taxfilepattern={'lsu' : "tax_slv_lsu_%s.diff",

                'ssu' : "tax_slv_ssu_%s.diff"
               }

This time the script started to work but crash later with this error message:

root@coldsunshine-Precision-Tower-7910:/home/coldsunshine/Desktop# obisilva --ssu --parc

Reading taxonomy dump file...

Sorting taxons...

Assigning parent taxids...

Traceback (most recent call last):

  File "/usr/local/bin/obisilva", line 324, in <module>
    options.taxonomy = SilvaDump(taxonomydata)

  File "/usr/local/bin/obisilva", line 212, in __init__
    self._readNodeTable(taxdump)

  File "/usr/local/bin/obisilva", line 255, in _readNodeTable
    taxonomy=[[n[0],n[1]]+ silvaPathParser(n[2]) for n in taxonomy]

  File "/usr/local/bin/obisilva", line 202, in silvaPathParser
    if x[1]=="":

IndexError: list index out of range

I looked into the line but I am not that good in python programming to figure out what is wrong.

Please need some help. Thanks