I have been trying to use metaphlan3 which was recently install by our HPC admins. I’m getting stuck at the first step of the tutorial.
When I run the following: metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt
I get the following error: Unable to create folder for database install: /usr/local/metaphlan/3.0/lib/python3.7/site-packages/metaphlan/metaphlan_databases
when I use --bowtie2db to point to a directory that I have write permissions for, the database files seem to download ok but the database build never finishes, it just stalls once it reaches a certain point. The following files are in the database directory where they should be, but one of the files “mpa_v30_CHOCOPhlAn_201901.2.bt2” is empty.
I run into the same issues when I try metaphlan --install.
Any ideas what may be going on?