CheckM2
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chklovski
Assessing the quality of metagenome-derived genome bins using machine learning
Hi, I'm having the following issue when trying to run checkm2: $ checkm2 database --download --path ./ Traceback (most recent call last): File "/anaconda3/miniforge-install/envs/checkm2/bin/checkm2", line 27, in from checkm2 import...
The installed checkm2 v1.0.1 returns an error saying that the model could not be loaded. `testrun` seems not working. Manual installation with checkm2 v1.0.2 by `git clone` and `python setup...
Hello, Just curious about whether CheckM2 can be fine-tuned to assess the eukaryotic microbial genome quality. Andy
In the script prodigal.py, when using numpy to index and slice the codingbase for masking (assigning as 1), should the indexing start from pos[0]-1?
How old is the uniref database that CheckM2 is currently using? I see a reference to 3rd june 2018 in the main publication but am not sure if it has...
Hello, When I submit the checkm2 command on the cluster using `sbatch`, I encounter different errors each time, __such as__ _`ERROR: Make sure prodigal is on your system path.`_ or...
Is the Diamond output file the annotation of the entire bin or is it the annotation of specific genes that checkm2 considers important for things like completeness/contamination calculations?
Here is the stack trace: (checkm21) abel@tll-rnode01:~$ checkm2 testrun [09/08/2023 05:49:58 PM] INFO: Test run: Running quality prediction workflow on test genomes with 1 threads. [09/08/2023 05:49:58 PM] INFO: Running...
Hello, I'm trying to install checkM2 on my Mac with conda, but when I do the testrun I see the following: ``` $ checkm2 testrun [02/27/2024 02:10:46 PM] INFO: Test...
I have a pretty unique installation. I have conda environments that I've built on an EC2 that are stored on EFS. I have a separate EC2 for submitting SLURM jobs...
