llk578496

Thank you for the fix! We tried to create a new environment named as `phylophlan-dev` with `python=3.10.6` with the below command. `mamba create -n phylophlan-dev python=3.10.6` Then, we cloned the...

The `phylophlan_setup_database` looks fine now! [phylophlan_setup_database.log](https://github.com/biobakery/phylophlan/files/9555832/phylophlan_setup_database.log)

Hi @rpetit3 Thank you so much for adding the `--dragonflye_opts`! We just tried to use it with the command below: `bactopia --ont --SE /mnt/data2/Food/REAL/02_fastq/Batch041_C_02_NS_XLDTT_01_Sub_01_Sub.fastq.gz --sample Batch041_C_02_NS_XLDTT_01_Sub_01_Sub --datasets /mnt/data2/Food/REAL/datasets --outdir /mnt/data2/Food/REAL/04_bactopia/04.1_tmp/Batch041_C_02_NS_XLDTT_01_Sub_01_Sub...

It works! Thank you so much for your help!

It would be great that if clonal_complex is included.

Hi @d4straub Sure! I am glad to contribute for this pipeline.