Hi,
I am new for using Humann 3.8 (the newest version on my university HPC) to run my functional analysis. I downloaded chocophlan and Uniref90 databases using the commands below:
wget https://g-227ca.190ebd.75bc.data.globus.org/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz -P path/to/my/database
wget https://g-227ca.190ebd.75bc.data.globus.org/humann_data/uniprot/uniref_annotated/uniref90_annotated_v201901b_full.tar.gz -P /path/to/my/database
I uncompressed the files above to put all the *.v201901_v31.ffn.gz files in a folder ‘cholophlan’ and a dmnd file to the folder ‘uniref90’
Then I wanted to run a single sample using:
module purge
module load humann/3.8
humann -i /my/pathway/to/inputdata/my_sample.fastq.gz
-o /my/pathway/to/outputdata/humann3_output
–input-format fastq.gz \
–nucleotide-database /path/to/my/database/chocophlan
–protein-database /path/to/my/database/uniref90
I always got an error: PermissionError: [Errno 13] Permission denied: ‘/apps/humann/3.8/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_latest’ → ‘/apps/humann/3.8/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_previous’
I tried prevent it updating the metaphlan_databases by adding another line:
–metaphlan-options “–offline”
Then get another error:
humann: error: argument --metaphlan-options: expected one argument
I wonder if I did anything wrong or still need to download some other databases? I also have taxnomic profiling outputs from Metaphlan 4.1.1, but not sure if they are compatible with Humann 3.8. If can be compatible, how to modify the commands to use my taxanomic outputs running the functional mapping instead of running Metaphlan again? If not, I am good with running Humann 3.8 with the older version of database v201901_v31, while need some guidance to solve the errors above. Thank you!