Metawibele preprocess fail

Microbial community profiling MetaWIBELE
22

Hi Yuzie,

Based on the error log, this issue seems to arise when loading the dependent databases. I am surprised that you ran the demo data successfully but failed using your input data. In theory, the process of loading the dependent databases should be independent of the inputs. When you tested the demo data and your input data, did you run them in the same computation environment (i.e. in the same system with loading the same dependent modules, in the same Python environment, etc.)? Some potential ways to debug this:

  1. Using exactly the same environment, test the demo data and your input data and see how they will perform.
  2. Please check whether there are some other errors before this step, and make sure the dependent inputs for this step are available.
  3. The default python of the current docker image is python2.7, while MetaWIBELE is implemented in Python3. It might lead to some incompatibility when loading models with Python 2. But it seems less possible since you ran the demo successfully unless your environment was changed when you run with your input data. You can set your default python as python3 in your docker env (e.g. “ln -s /usr/bin/python3.6 /usr/bin/python”).

Best,
Yancong

23

Dear Yancong,
Actually, I build your docker container from your image on my desktop image first and tested your test file (only the characterize and prioritize steps)
And I wrapped up the container to image to my lab server. ( I was using docker export to metawibele.tgz file) When I tried on our in-house data the first worked but failed in characterize step. Besides, I didn’t test the test dataset in our server environment. I will try your way to see the error, and will update you the outcome.

Thank you for all of your help :relaxed:,
Yuzie

取得 Android 版 Outlook

24

Hello Yancong,

I first “rm /usr/bin/python” and then “ln -s /usr/bin/python3.6 /usr/bin/python”.
The characterization step went smoothly ~~~
The python version is the reason why we confronted with this step crush.
Maybe, next docker version you can change the environment python version !

THANK YOU !!
Yuzie

25

Hi Yuzie,

Great, thanks for updating me on your progress! We added this type of feedback to our list and will make more tweaking in the future docker version.

Best,
Yancong