Regarding SPacc

[Shahista Jan]

Hello Team 

I know that Sparcc is not a part of QIIME but I personally think that this is the best platform from where I can get my answer. 

I want to do co-occurance analysis of my OTUs.

While going through the tutorial I am successfully done upto some steps 

i.e the biom convert steps and the "Now remove the first line of the taxon file"  i.e sed 1 

How ever while running the command 

python ../../../sparcc/SparCC.py biom-converted_22 ( the name of my file)

I am getting this error 

reading data

Traceback (most recent call last):

  File "sparcc/SparCC.py", line 318, in <module>

    counts = read_txt(counts_file)

  File "/home/qiime/sparcc/io_methods.py", line 54, in read_txt

    temp = read_table(file, **kwargs)

  File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 465, in parser_f

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 241, in _read

    parser = TextFileReader(filepath_or_buffer, **kwds)

  File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 557, in __init__

    self._make_engine(self.engine)

  File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 694, in _make_engine

    self._engine = CParserWrapper(self.f, **self.options)

  File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 1061, in __init__

    self._reader = _parser.TextReader(src, **kwds)

  File "pandas/parser.pyx", line 512, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:4792)

ValueError: No columns to parse from file

 Please suggest....

[Muneer Malla]

Dear Shashita
Yes SPracc is not a part of QIIME, I think it is simply a bunch of scripts that you need to perform.
Moreover be patient some one will sort it for you