Regarding SPacc

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Shahista Jan

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Mar 2, 2020, 1:47:29 PM3/2/20
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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

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Mar 3, 2020, 4:51:53 AM3/3/20
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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
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