Hi! I know there are other open questions on this topic, but as I am using the latest version of Humann (3.6) I wanted to open a new issue. I am currently going through the setup process of Humann in a conda environment, and followed the steps on your installation guide and ran the following commands:
conda create --name biobakery3 python=3.7 conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --add channels biobakery conda install humann -c biobakery``` I then downloaded all the databases: humann_databases --download chocophlan full /scratch4/jsuez1/week12/chocophlan --update-config yes humann_databases --download uniref uniref90_diamond/scratch4/jsuez1/week12/diamond --update-config yes humann_databases --download utility_mapping full /scratch4/jsuez1/week12/diamond --update-config yes
Then when I try to run either a sample of mine or the demo.fastq.gz, i get this error:
Running metaphlan ........ CRITICAL ERROR: Error executing: /home/hhallow1/.conda/envs/biobakery3/bin/metaphlan /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/tmpm6r5uqir/tmpe2u0gnbk -t rel_ab -o /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bowtie2.txt Error message returned from metaphlan : No MetaPhlAn BowTie2 database found (--index option)! Expecting location bowtie2db Exiting...
I have tried deleting and re-installing the databases, i’ve tried updating the config file (it was already updated), i’ve tried completely re-installing humann in a new environment and im not sure what else to do. i’ve used humann in the past with no problems at all. any help would be appreciated! Thanks!