Can anyone please explain the meaning of this error?

327 views
Skip to first unread message

Sai Prabhas Konduru

unread,
Jan 5, 2018, 11:21:20 AM1/5/18
to Qiime 1 Forum
Hello I tried to run QIIME using a few samples and a negative control with no bacteria. But the results were surprising as I found more bacteria identified under negative control than the samples which shouldn't be the case. This is the error log.

discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
/usr/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):
/usr/miniconda3/envs/qiime1/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):
discarding /usr/miniconda3/bin from PATH
prepending /usr/miniconda3/envs/qiime1/bin to PATH
/usr/miniconda3/envs/qiime1/lib/python2.7/site-packages/numpy/core/_methods.py:82: RuntimeWarning: Degrees of freedom <= 0 for slice
  warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning)

It would be a great help if anyone can figure this out.

Colin Brislawn

unread,
Jan 5, 2018, 9:37:40 PM1/5/18
to Qiime 1 Forum
Hello,

Happy New Year!

The error log is mostly warnings (instead of errors), so I think this scripts worked well.

Understanding why reads appeared in your negative control can be tricky. It could be sample contamination, a mistake with demultiplexing, or something else. Take a look at this conversation in the Qiime 2 forums where we discuss what to do with reads in your negative control:  


Have you considered using Qiime 2? The new version of qiime comes with plugins to work with control samples. You could consider upgrading, then posting your questions about Qiime 2 on the Qiime 2 forums. 

Colin

Reply all
Reply to author
Forward
0 new messages