Metaphlan not running at all

I installed metaphlan4 using conda and have installed the database to a directory in my home folder. However, when I run metaphlan, I don’t get any output. No logs, nothing. it only creates an empty bowtie2out.txt file.

the command I am running is
metaphlan trimmed-SW46_1.fq --bowtie2db /scratch/Database_folder/ --input_type fastq -o trim46_profile.txt --biom trim46_biom.txt --nproc 48.

What am I doing wrong?

Hi @OluchiAroh
Does the same behaviour happen when running metaphlan trimmed-SW46_1.fq --bowtie2db /scratch/Database_folder/ --input_type fastq --biom trim46_biom.txt --nproc 48 > trim46_profile.txt ?

Hi @aitor.blancomiguez

That worked! Thank you so much

One more question, is there a way I can merge the biom outputs together?. I need one biom file for all my samples.

Hi @OluchiAroh
Unfortunatelly, metaphlan does not include a merging script for the biom output