Humann error with metaphlan


I ran the following code and got error: humann --input-format fastq.gz --input /analysis_results/bwa_meme_results/Remove_host_merge1.fq.gz --output /analysis_results/Humann/Humann_1 --threads 128 --metaphlan-options “–bowtie2db /Reference_database/metaphlan”

Metaphlan itself works well. But, when I used Humann, it failed.

Does anyone know why and how to solve the problem?

The Error I got:

  • Output files will be written to: /analysis_results/Humann/Humann_1

  • Decompressing gzipped file …

  • Running metaphlan …

  • ERROR: The relative abundance and coverage were not found in the MetaPhlAn taxonomic profile. Please run MetaPhlAn with the option(s): --bowtie2db /Reference_database/metaphlan.

What version of HUMAnN are you using?

I am using humann v4.0 and metaphlan/4.1.0.

HUMAnN 4 has not been released yet. It notably calls MetaPhlAn with some different options than we’ve used in the past, which might be related to the error you’re seeing here.

Thank you! Will you suggest me to use Humann 3.9 instead?

Yes, that is the most recent released version, and is compatible with the latest MetaPhlAn. I will make an announcement here when HUMAnN 4 is available. We are still troubleshooting an aspect of the translated search procedure in that version.