Closed JustinGibbons closed 1 year ago
Creating the environmental variable CHECKM2DB as describe in the checkm2 documentation does solve the problem, but I still don't know why atlas wasn't able to find the database in the first place
I ran into the same issue with the identify rule. I solved it by creating the GTDBTK_DATA_PATH similar to what is described here: https://ecogenomics.github.io/GTDBTk/installing/bioconda.html
Instead of adding it to the conda env I added export GTDBTK_DATA_PATH to the bash script I use to submit the atlas job
I will check this.
I saw that there just came out a new small update to checkm2 db.
Could you tell me in which rule you had the gtdb error.
I also saw that you use not the latest atlas version. I think at least the gtdb errer should ve fixed in it.
Hi Silas,
The gtdb error was in rule identify.
Does atlas update the conda environment everytime there is an update to a package?
I follow the recommended environment definitions. I specify the tools' major and minor versions. This lets some room for bug fixes.
e.g. I defined - checkm2>=1.0.1, <1.1
So you could have 1.0.1 or 1.0.2 installed.
Could you please use
conda activate /work/j/jgibbons1/Tina_Sample_Metagenome_Atlas/conda_envs/c5f2f8c426b3efe91c8be14f2a13c9c0_
conda list checkm
and tell me the version of checkm2 you are using.
If it is 1.0.1
you might run
rm -r /work/j/jgibbons1/Tina_Sample_Metagenome_Atlas/conda_envs/c5f2f8c426b3efe91c8be14f2a13c9c0_
and then run atlas.
Hi Silas,
This is the checkm version information
Name Version Build Channel
checkm2 1.0.1 pyh7cba7a3_0 bioconda
The job I just ran was too big to do again now that it's finished, but I'll try your suggestion if I run into problems again.
Thank you
Here is the relevant log output:
The checkm2.log file says:
Atlas version atlas, version 2.14.2 Snakemake 7.18.2 Additional context This seems like a straightforward error except the database does exist. I have uniref100.KO.1.dmnd downloaded and I previously did a successful test run using the downloaded databases. Also eggNOG is successfully finding it's databases.
According to the checkm2 documentation you can use an environmental variable to tell checkm2 where the databases are: https://github.com/chklovski/CheckM2
I can test this out and report back, but I thought you'd like to know about this error.
Do you know any other ways I can get atlas to find the checkm2 database?
Thank you