Humann error with metaphlan

Microbial community profiling HUMAnN
1

Hi,

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.

2

What version of HUMAnN are you using?

3

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

4

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.

5

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

6

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.