Amazing tool. Very excited to use it! I would like to ask a few questions, but first I will give an overview of my experience:
I have installed the EukRep pipeline with pip in a virtualenvironment of Python3.5
I tried to run and it said it had no scipy. So I installed with pip as well (maybe an update could include the pip install scipy).
Then I tried to run with some sample data I have here:
$ EukRep -i EM27_S12_L001_R1_001.fastq -o test --prokarya prokarya_file
And I got the following message:
/home/brizolat/tools/eukrep/eukrep/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
The output files were empty.
Questions:
1) My input data are fastq forward reads. Should the input be a file with interleaved reads (forward and reverse) or, instead, the reads after mergind (with pandaseq or pear, for example)?
2) The problem I got was something with my data or with the script itself? Maybe you could provide us with some example input data to test the if the installation is correct?
3) How can I fix it? =)
Again, thank you very much for the tool and for the given attention.
Dear Patrick,
Amazing tool. Very excited to use it! I would like to ask a few questions, but first I will give an overview of my experience:
$ EukRep -i EM27_S12_L001_R1_001.fastq -o test --prokarya prokarya_fileAnd I got the following message:
The output files were empty.
Questions: 1) My input data are fastq forward reads. Should the input be a file with interleaved reads (forward and reverse) or, instead, the reads after mergind (with pandaseq or pear, for example)? 2) The problem I got was something with my data or with the script itself? Maybe you could provide us with some example input data to test the if the installation is correct? 3) How can I fix it? =)
Again, thank you very much for the tool and for the given attention.
Best, Rodolfo