humann2_barplot ValueError

[brianf...@gmail.com]

Hello,

I am trying to create a barplot from a humann2 pathabundance.tsv and get the following error:

Traceback (most recent call last):
File "/Users/carlsonlab/anaconda2/bin/humann2_barplot", line 11, in <module>
load_entry_point('humann2==0.11.1', 'console_scripts', 'humann2_barplot')()
File "/Users/carlsonlab/anaconda2/lib/python2.7/site-packages/humann2/tools/humann2_barplot.py", line 336, in main
exclude_unclassified=args.exclude_unclassified,
File "/Users/carlsonlab/anaconda2/lib/python2.7/site-packages/humann2/tools/humann2_barplot.py", line 217, in __init__
self.update( )
File "/Users/carlsonlab/anaconda2/lib/python2.7/site-packages/humann2/tools/humann2_barplot.py", line 220, in update
self.nrows, self.ncols = self.data.shape
ValueError: need more than 1 value to unpack

It appears that for some samples the "values" variable in FeatureTable.__init__ is not being initialized properly and the resulting values passed to self.nrows, self.ncols = (0,)

Command Run:
humann2_barplot.py -i PWY-6126.tsv -f PWY-6126 -m Antibiotics -l Antibiotics -k PuBu -o PWY-6126.png

Thank you,
Brian

[Eric Franzosa]

Hi Brian,

It's not obvious to me from the error message alone what the root cause is. If you're willing to share your input file with me (feel free to reply individually) I would be happy to take a closer look.

Thanks,

Eric

[Brian Fochtman]

Thanks Eric. On the interface I could not find a way to attach a file.

I've attached one example that fails.

[Eric Franzosa]

OK, I think I see the issue. The barplot script is specifically looking to plot the stratifications of a function, and it looks like you're only giving in the community total (possibly because there were no stratifications)? For example, if you have a function A:

Feature Abund

A          10   

A|1         6

A|2         4

The script would actually just be plotting the stratified values (6 and 4) and not using the total. I will fix the script so that it gives a more helpful error message in this case.

Thanks,

Eric

[Brian Fochtman]

Thank you for your help.