RuntimeError

[DHelix]

Hi!

I created a python virtual environment using conda, and installed arboreto using the conda package manager.
I downloaded example files (from here https://github.com/tmoerman/arboreto/tree/master/resources/dream5/net1) and was trying to run run_grnboost2.py. I got the following error:

Exception ignored in: <generator object add_client at 0x1c1ca87830>
RuntimeError: generator ignored GeneratorExit
tornado.application - ERROR - Exception in Future <Future cancelled> after timeout
Traceback (most recent call last):
  File "/projects/djin_prj/Installs/conda/arboreto/lib/python3.6/site-packages/tornado/gen.py", line 970, in error_callback
    future.result()
concurrent.futures._base.CancelledError

Despite showing an error, it created an output file with 318832 lines.

I also created a python virtual environment using virtualevn, and installed arboreto using pip.
I ran the same run_grnboost2.py and it didn't report any error. It also create an output file with 318827 lines (fewer lines compared to the provious one).

Given the second output file containing fewer lines of result, I wasn't sure if the second method worked successful, or it also stopped in the middle but somehow didn't show any errrors on screen...

Could you please help me? Thanks!

UPDATE:
I ran run_grnboost2.py in the virtual environment created by virtualevn (the second method). Again, it didn't show any error, and created an output file. But this time the output file contained 318779 lines. I don't think arboreto finished successfully...

[tmoerman]

Hello,

it is normal that in different runs, a (slightly) different number of output lines is generated. The reason for this behaviour is that stochastic machine learning methods are used (gradient boosted decision tree regression). The general trends (strong predictors for a target gene) will be stable though.

I'm pretty sure the program is working correctly.
In general Tornado errors are occasionally thrown, you can safely ignore these.

regards,
Th.

[DHelix]

Hi Thomas,

I really appreciate your prompt reply!
Aha, I see. thanks for the explanation of the number of output lines.
I actually ran arboreto in the first virtual environment (created using conda) a few times and the Tornado errors showed every time, not just occasionally... Maybe I should stick with the second installation?

Thanks!