Hello!
I’m using two environments: local and EC2
Locally after several attempts I managed to get it run, but It’s been impossible to get the same exact example to run in a EC2 instance
I have all the DB files installed both in the default location but also in a personalized file
I have tried every possible combination of the parameters --index and --bowtie2db
When I try specifying the index or the db path, the error persists even in a folder i SET UP
Try removing all the files in metaphlan_databases folder and redownloading the database with metaphlan --install because it seems like you are missing some bowtie2 database files.
Also, you have to specify the parameters before you redirect the output to file with >.
You would have something like metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta --nproc 12 --bowtie2out SRS014476-Supragingival_plaque.bowtie2out > SRS014476-Supragingival_plaque_profile.txt
