error in test_checkm.py

[yb5339]

Hi, I tried to run the new version of MAGpy, and I got an error in running tests. When the step testing test_checkm.py, the terminal stopped and nothing happened. All the other testing steps were well processed.

❯ snakemake -rp -s MAGpy --cores 120 --use-conda test The flag 'directory' used in rule all is only valid for outputs, not inputs. Building DAG of jobs... Using shell: /bin/bash Provided cores: 120 Rules claiming more threads will be scaled down. Job counts: count jobs 1 test 1 test_checkm 2 Select jobs to execute...

[Thu Jun 3 20:08:44 2021] rule test_checkm: output: test/outputs/checkm.txt jobid: 2 reason: Missing output files: test/outputs/checkm.txt

    test/scripts/test_checkm.py test/outputs/checkm.txt 

Activating conda environment: /home/yb/MAGpy/.snakemake/conda/193fb18dbd5d570d4fcebaa03389205a

How can I solve this problem? Thank you!

[mw55309]

Hey

I would start by activating the environment:

conda activate /home/yb/MAGpy/.snakemake/conda/193fb18dbd5d570d4fcebaa03389205a

Then trying first to see if checkm runs:

checkm

Then trying to see what happens if you run the test script

test/scripts/test_checkm.py test/outputs/checkm.txt

[yb5339]

@mw55309 I try to activate "conda /home/yb/MAGpy/.snakemake/conda/193fb18dbd5d570d4fcebaa03389205a" and run checkm. Then I can see the message like below...

 ❯ checkm
It seems that the CheckM data folder has not been set yet or has been removed. Running: 'checkm data setRoot'.
Where should CheckM store it's data?
Please specify a location or type 'abort' to stop trying:

So I try to run "❯ checkm data setRoot", and the results were same as above.

I also running "❯ test/scripts/test_checkm.py test/outputs/checkm.txt", and nothing happened...

[mw55309]

And what are the contents of test/outputs/checkm.txt?

[yb5339]

When I run test_checkm.py, it never ends. So there is no text in test/outputs/checkm.txt (0 bytes).

[mw55309]

Sorry, this should have been fixed in the recent commit