The bioBakery help forum

Humann3 log output error

Hello,
I’ve been running humann3 alpha version and run into some problems.

  1. 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.
  2. Here is my batch code:

conda init bash
export CONDA3PATH=/mnt/home/shenyike/anaconda3
module load Conda/3
conda activate biobakery3
cd /mnt/ls15/scratch/users/shenyike/FOLDER/humanndemo
/mnt/home/shenyike/.local/lib/python3.6/site-packages/metaphlan/metaphlan_databases
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
conda deactivate

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!!

Hello - Thank you for your detailed post and sorry for the slow response! The HUMAnN software outputs INFO/DEBUG messages to the log to record additional information that is not printed to stdout out. This information can be used to debug runs if needed. You can tune your log output level using the option --log-level <LEVEL> to capture more or less output to the log if needed. Looking at the screenshots you captured I don’t see any errors. If you would provide the error messages or the full log I can help debug what might be up.

Thank you,
Lauren

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