Humann4 not recognizing relab column in metaphlan4 table

Microbial community profiling HUMAnN
1

Hi there.I was wondering if I can get help with an issue I’m encountering.
I’ve been using Humaan4 and metaphlan4 and “mpa_vOct22_CHOCOPhlAnSGB_202403” database.
when I run my humann script as
humann \

    --input ${INPUT_FASTQ} \\

    --input-format fastq \\

    --output ${SAMPLE_OUTPUT} \\

    --nucleotide-database ${HUMANN_DB}/chocophlan \\

    --protein-database ${HUMANN_DB}/uniref \\

    --metaphlan-options "-t rel_ab_w_read_stats  -x mpa_vOct22_CHOCOPhlAnSGB_202403  --bowtie2db ${METAPHLAN_DB}" \\

    --threads 16 \\

    --resume \\

    --verbose

I get the error below:
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 -x mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2db /projects/b1180/db/metaphlan_db_vOct22.

Although when I check the mpa4 table produced it indeed includes the relab

here is the header for mpa4 output:

#mpa_vJun23_CHOCOPhlAnSGB_202403
#/software/metaphlan/4.0.1/bin/metaphlan /projects/b1042/HartmannLab/Hauser-mice/output/humann/cat/BC-10_CK1D-5_S10_combined.fastq -t rel_ab_w_read_stats -x mpa_vJun23_CHOCOPhlAnSGB_202403 --bowtie2db /projects/b1180/db/metaphlan_db_2024 -o /projects/b1042/HartmannLab/Hauser-mice/output/humann/BC-10_CK1D-5_S10/BC-10_CK1D-5_S10_combined_1_metaphlan_profile.tsv --input_type fastq --bowtie2out /projects/b1042/HartmannLab/Hauser-mice/output/humann/BC-10_CK1D-5_S10/BC-10_CK1D-5_S10_combined_humann_temp/BC-10_CK1D-5_S10_combined_metaphlan_bowtie2.txt --nproc 16
#SampleID Metaphlan_Analysis
#estimated_reads_mapped_to_known_clades:16153433
#clade_name clade_taxid relative_abundance coverage estimated_number_of_reads_from_the_clade

2

It looks like the MetaPhlAn profile was generated with the mpa_vJun23_CHOCOPhlAnSGB_202403 database (from the header) but it should be mpa_vOct22_CHOCOPhlAnSGB_202403 for the current HUMAnN (matching your command). So your custom MetaPhlAn options look correct, but the taxonomic profile you’re starting from was not run on the correct marker database. For troubleshooting this sort of thing it can sometimes be easier to run MetaPhlAn outside of HUMAnN (using the command you specified) and then pass the resulting taxonomic profile to HUMAnN via the --taxonomic-profile flag.