Missing relative abundance and coverage error for humann4a

Microbial community profiling HUMAnN
1

humann v4.0.0.alpha.1
MetaPhlAn version 4.0.0 (22 Aug 2022) (also attempted with 4.1)

Hi! I’m attempting to get the humann v4.0.0.alpha1 package working using the demo file, and am encountering an error. Specifically, “ERROR: The relative abundance and coverage were not found in the MetaPhlAn taxonomic profile.”

My command is: humann -i demo.fastq -o sample_results/ --metaphlan-options=“–input_type fastq --bowtie2db /rs1/researchers/c/cmtherio/02_Lab_Member_Folders/Gancz_Abigail/programs/biobakery4/database -x mpa_vOct22_CHOCOPhlAnSGB_202403 -t rel_ab_w_read_stats”, and the metaphlan_profile that is output has the following columns:

#clade_name clade_taxid relative_abundance coverage estimated_number_of_reads_from_the_clade

This seems to suggest that it is generating the proper information, but that it isn’t detected for some reason.

Has anyone encountered this issue, or knows how to resolve it?

Thanks!

2

Which demo file are you using? The one associated with the HUMAnN 3 tutorial might not have any bugs found by MetaPhlAn 4, hence the empty output file. There is a new demo file in the HUMAnN 4 repo:

But I still need to update the tutorial docs / create a new v4 tutorial around this file. Probably in the next couple of months.