Hi,
I’m encountering an issue with MetaPhlAn version 4.1.0 (23 Aug 2023), where it seems to go back to the default database path despite specifying the database path using the --bowtie2db parameter in my script. Here’s a part of my code:
metaphlan $file --input_type fastq
–bowtie2out “$file_output/${1}_metagenome.bowtie2.bz2”
–nproc 40
-o “$file_output/${1}.txt”
–bowtie2db “/home01/data/biobakery/metaphlan/”
–index “mpa_vJun23_CHOCOPhlAnSGB_202307”
I receive the following error message:
[Error] The default MetaPhlAn database cannot be found at: /home01/apps/anaconda3/envs/biobakery4/lib/python3.7/site-packages/metaphlan/utils/…/metaphlan_databases/mpa_latest
Even though I’ve specified --bowtie2db with the correct path, MetaPhlAn still tries to use the default database path. Could anyone please advise on how to ensure that MetaPhlAn uses the specified database path correctly?
Thank you.