I’ve been running humann3 alpha version and run into some problems.
- At first, there are some package conflicts in my conda resulting in output (log file and my slurm output) error, so I uninstalled my anaconda3 2019 version and installed new anaconda3 2020.11 version. I successfully reintalled humann3 in new environment I built in new conda. However, the problem continues.
- Here is my batch code:
conda init bash
module load Conda/3
conda activate biobakery3
humann_config --update database_folders nucleotide /mnt/home/shenyike/.local/lib/python3.6/site-packages/metaphlan/metaphlan_databases/chocophlan
humann_config --update database_folders protein /mnt/home/shenyike/.local/lib/python3.6/site-packages/metaphlan/metaphlan_databases/uniref
humann_config --update database_folders utility_mapping /mnt/home/shenyike/.local/lib/python3.6/site-packages/metaphlan/metaphlan_databases/utility_mapping
humann -i SAMPLE.fastq.gz -o fastq_SAMPLE_1204full --threads 4
This batch was able to run however it output lots of debug and error messages, unlike what showed in the demo. Please see the few screenshots attached.
Does anybody know what happens here? Thank you!!