Issue running test data

[BenLRoss]

Hello,

I tried running the example data with the command python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f in the ViralRecall conda environment and was returned this error message after it ran to completion:

Traceback (most recent call last): File "viralrecall.py", line 733, in <module> status = main() File "viralrecall.py", line 728, in main run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "viralrecall.py", line 655, in run_program plt.ylim(minval, numpy.nanmax(df2["rolling"])) File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/matplotlib/pyplot.py", line 1478, in ylim ret = ax.set_ylim(*args, **kwargs) File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/matplotlib/axes/_base.py", line 3470, in set_ylim if bottom == top: File "/media/imperator/bross/miniconda3/envs/ViralRecall/lib/python3.5/site-packages/pandas/core/generic.py", line 1576, in __nonzero__ .format(self.__class__.__name__))

Is this an issue regarding the installed versions of matplotlib (3.0.0) and pandas (0.23.4) in the environment?

[faylward]

Yes this looks like a matplotlib error- I would try with a different Python version (tested on 3.5.6) and see if it still comes up. If you don't need the plot you could also try removing the -f flag and seeing if it persists.

[BenLRoss]

The environment is installed with Python 3.5.6, and we were able to get the run to complete without the -f flag. What version of matplotlib was tested?

[faylward]

It was tested on Python 3.6.12 running matplotlib 3.3.4 and Python 3.5.6 running matplotlib 3.0.0. In both cases this was done on CentOS Linux release 7.4.1708.

[faylward]

if it helps I also just tested it on Ubuntu 16.04.7, python 3.5.6, matplotlib 3.0.3

[BenLRoss]

Sorry for the lapse in response, but I was able to get it to run with matplotlib 3.0.3. Thank you!