Error in QQ plots

[Charlie Repaci]

Hello pheweb team,

I have a bit of a basic question, but I've gotten an error in the QQ plots which I'm not sure how to fix. The rest of the files seem to have been created just fine, but when the browser is served, none of the phenotypes appear.

The initial output shows:

==> Starting `pheweb qq` Processing 43 phenos

WARNING: got gc_value inf

[... many repeats of the same warning ...]

WARNING: got gc_value inf

Completed 0 tasks in 0 seconds (42 currently in progress, 43 remain)

==> failed after 1 seconds Child process had exception, info dumped to [path]

The detailed error file shows:

Child process had exception:
   math domain error
Traceback:
   Traceback (most recent call last):
     File "/usr/local/lib64/python3.6/site-packages/pheweb/load/load_utils.py", line 250, in f
       x = do_single_task(task)
     File "/usr/local/lib64/python3.6/site-packages/pheweb/load/qq.py", line 58, in make_json_file
       rv['ci'] = list(get_confidence_intervals(len(variants)))
     File "/usr/local/lib64/python3.6/site-packages/pheweb/load/qq.py", line 189, in get_confidence_intervals
       'x': round(-math.log10((variant_count-0.5)/num_variants),2),
   ValueError: math domain error

Is this just an issue with the libraries I have loaded? I appreciate any help you can offer.

Thanks so much!

[Charlie Repaci]

I've figured out the issue! My teammate passed me a small subset of the data to work with which only included one variant for some of the phenotypes. After these were excluded, it ran as intended.