MetaPhlAn no relative abundance hnn4

Microbial community profiling HUMAnN
1

Hi,
I was trying to run HUMAnN v4.0.0.alpha.1 installed following this guide (HUMAnN 4.0.0.alpha.1 Release Notes - Google Docs), but the software crashed after running MetaPhlAn prompting the folowing 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): --index mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2db /path/to/mpa/database.

I checked the taxonomic profile produced and it was fine.
Here the first couples of lines of the profile:

#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Bacteria 2 100.0
k__Bacteria|p__Firmicutes 2|1239 84.08941
k__Bacteria|p__Bacteria_unclassified 2| 12.284
k__Bacteria|p__Bacteroidetes 2|976 2.08048
k__Bacteria|p__Proteobacteria 2|1224 1.05261
k__Bacteria|p__Actinobacteria 2|201174 0.4935
k__Bacteria|p__Firmicutes|c__Clostridia 2|1239|186801 83.5216
k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified 2|| 12.284
k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 2.08048
k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 2|1224|28216 1.05261
k__Bacteria|p__Actinobacteria|c__Coriobacteriia 2|201174|84998 0.4935
k__Bacteria|p__Firmicutes|c__CFGB6645 2|1239| 0.32166
k__Bacteria|p__Firmicutes|c__CFGB74538 2|1239| 0.18445
k__Bacteria|p__Firmicutes|c__CFGB74524 2|1239| 0.0617

The databases I used were those suggested in the release note, in particular:

  • mpa → mpa_vOct22_CHOCOPhlAnSGB_202403

Here the code I used:

humann --input /path/to/input/sample.fastq --output /path/to/output/ --nucleotide-database /path/to/nucleatide/database/chocophlan/ --protein-database /path/to/uniref/database/uniref --threads=16 --remove-temp-output --utility-database /path/to/utility/database/utility_mapping --o-log /path/to/output/sample.log --metaphlan-options “–index mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2db /path/to/mpa/database”

In the pasted command lines, I masked my directories paths for data confidentiality, obviously when I ran the command I used the real paths.

Any idea why the software crashed?

I previously ran hnn3.9 on the same sample and it worked correctly.

Thanks

2

I think the issue is because HUMAnN 4 now runs MetaPhlAn 4 using the -t relab_with_read_stats mode to get estimated SGB coverage. If you’re using the --metaphlan-options flag to specify arguments to the MetaPhlAn command, you would probably need to include the -t flag as well. Try that and let us know if it resolves the issue?

3

Hi,
by adding the flag -t relab_w_read_stats the software ran correctly!

Thanks