CRITICAL ERROR: Can not find file /beegfs/home/wanglu/IBD/multiIBD/sample_results/demo_humann_temp/demo_metaphlan_bugs_list.tsv
I am living in China, so database files stored in dropbox might cause problem, however, I manage to find those files.
If you are using the --metaphlan-options flag to pass information to MetaPhlAn then string that follows has to be a valid set of MetaPhlAn options. For example, if you wanted to point MetaPhlAn at a specific database, you’d need to provide the MetaPhlAn flag for that option AND the path to the database.
You can verify that your MetaPhlAn options work as intended by running MetaPhlAn external to HUMAnN first. You can then pass those same options to HUMAnN with the --metaphlan-options flag OR, if you’ve already run MetaPhlAn on all your samples, pass those profiles to HUMAnN with the --taxonomic-profile flag.