Silas Kieser

Great thank you very much for your experience. Congratulations on your article. I think I should start listing the publication using atlas. Have you tried to use the bbmap 'best'...

Is there any more information about where in the code this issue arises. In the snakemake log when it's written, that the rule fails. it should print the path to...

Maybe we should update dram there is now a version 1.3.

## Hack: In the config file you can comment out the following two lines, wich allows to finish the rest of atlas. ``` annotations: - gtdb_tree - gtdb_taxonomy - genes...

Yes skitbio uses sklearn which raises an error. So the problem is probably in skit bio. I think the python version is too recent.

Thank you for the feedback @bcpd . I think the error is related to the too new version of python. On my side @507 worked on a test run I...

I also encountered this error. I try to solved it derectly in scikit bio but it is not solved. You can do: ``` conda activate /home/nwezejus/Peat_metagenome2022/ATLAS/databases/conda_envs/140c117b8fe5c17c29da39e6b9fb5794 conda install -y scipy=1.8...

Thank you for the question. You can do a hybrid assembly (ilumina + nanopore) using spades. I don't have experience of nanopore assembly alone. Maybe we can adapt atlas to...

Do you have only mate-pair libraries or in combination with normal-paired-end libraries? If you have only mate-pair libraries, as I understand, they can be mapped as normal paired-end libraries. It...

Ok then you could do it the following: Start Atlas with the single end read library `atlas init` . Set `spades_preset: normal ` in the config file to use normal...