RecursionError: maximum recursion depth exceeded in __instancecheck__

[chklovski]

RecursionError: maximum recursion depth exceeded in __instancecheck__

[chklovski]

Hi,

does checkm2 testrun complete successfully?

[B-1991-ing]

Hi Alex,

I ran the following command lines on the HPC as shown below, same errors.
module load tools computerome_utils/2.0
module load anaconda3/2021.11
module load checkm2/20220719
checkm2 testrun
checkm2 database --download --path DIAMOND_db

Error:
RecursionError: maximum recursion depth exceeded in instancecheck

Best,

Bing

[B-1991-ing]

When I opened the /services/tools/checkm2/20220719/bin/checkm2, is the installed checkm2 file correct?

[B-1991-ing]

The conversation between me and my HPC admin.

I email my HPC admin firstly as below,

Then, my HPC admin replied me as below,

[madscort]

Did you find a solution to this?

[B-1991-ing]

Not yet.
I want to use the checkm to assess my assembled MAGs, due to it not worked, I used the metawrap bin_refinement to refine the bins and get the checkm results assessed by the older version checkm.

[chklovski]

Hi, what python version are you using?

[B-1991-ing]

Hi Alex,

I am using python 3.9 installed under the anaconda3/2021.11 now.

anaconda3/2021.11: Anaconda3 2021.11 - Python 3.9 distribution for scientific computing

Best,,

Bing

[chklovski]

Hi, is this still an issue with the latest (1.0.1) version? Does it occur with the bioconda or pip install?

[B-1991-ing]

Thank you very much for message.

I am not sure there is still any problem with the latest version --- 1.0.1, as the HPC administrator didn't reinstall it since last august.

I can't manage to use the software due to this error last august and I didn't try the latest version this year.

Our HPC administrator installed using bioconda normally.

[chklovski]

Hi - bioconda installation wasn't available last august and was only added early this year. I would encourage you to install it that way as it's much more stable.