The bioBakery help forum

Metaphlan3 not taking input file

I’m trying to run samples with metaphlan3 that ran just fine with metaphlan2. I ran the command

% metaphlan --input_type fastq /opt/water/concatenated/19040D-02-01_S43_L004.fastq

and metaphlan just hangs as if it’s waiting for input from the keyboard. Why does it do this? I’m running

% metaphlan --version
MetaPhlAn version 3.0 (20 Mar 2020)

Thanks.

Daniel

i met the same error. Have you got the slution? Could you share your commands ?

(metaphlan-3.0) [students@Nebula metaphlan2_analysis]$ metaphlan3.py SRS014459-Stool.fasta.gz --input_type fasta --nproc 4 > SRS014459-Stool_profile.txt

-bash: metaphlan3.py: command not found