Error with the examples files

Microbial community profiling HUMAnN
1

Hello,
I’m having some problems with the examples files. I want to run HuManN (v4.0)

humann --input "$fastq_file" --output "$sample_output_dir"

But I always have this error

humann.search.prescreen - ERROR: The relative abundance and coverage were not found in the MetaPhlAn taxonomic profile. Please run MetaPhlAn with the option(s): -t rel_ab_w_read_stats.

So I tried with:

humann --input "$fastq_file" --output "$sample_output_dir"  --metaphlan-options="-t rel_ab_w_read_stats"

humann --input "$fastq_file" --output "$sample_output_dir"  --metaphlan-options="-t rel_ab"

humann --input "$fastq_file" --output "$sample_output_dir"  --metaphlan-options="-t reads_map"

But I always have the same error, and nothing changes. Do you have any idea? Because I have metaphlan --version MetaPhlAn version 4.0.0 (22 Aug 2022)
and if I run it alone, I do not have any errors!

Thank you

2

Sorry for the slow reply. Something about this is strange since HUMAnN should automatically be calling MetaPhlAn and asking for the extra read stats. This sort of error would occur if (e.g.) you ran MetaPhlAn outside of HUMAnN without asking for read stats and then tried to feed the resulting MetaPhlAn output to HUMAnN. I’m assuming that is not the case here?

It sounds like HUMAnN finishes running MetaPhlAn before it hits this error. Are you able to share the MetaPhlAn output here?