Humann 3.9 conda install will not work. Please update your version of MetaPhlAn?

Microbial community profiling HUMAnN
4

@franzosa ,

An update to my post.

I realized my MetaPhlAn 4.0.6 is actually older than vJun23 database support, and that is the real problem. So I did the following:

$ conda remove metaphlan

$ conda install metaphlan=4.1

$ conda install humann=3.9

Then, Reinstall the database

$ metaphlan --install --index mpa_vJun23_CHOCOPhlAnSGB_202307 --bowtie2db humann3_db/metaphlan_db_vJun23

I was able to run the metaphlan test using:

$ metaphlan --input_type fastq examples/demo.fastq.gz --bowtie2db humann3_db/metaphlan_db_vJun23 --index mpa_vJun23_CHOCOPhlAnSGB_202307 -o test.txt

where test.txt starts with #mpa_vJun23_CHOCOPhlAnSGB_202307 as expected

but still can’t run the humann demo test:

humann -i examples/demo.fastq.gz -o examples/SAMPLE2 --threads 16 --protein-database humann3_db/uniref --nucleotide-database humann3_db/chocophlan --metaphlan-options “–bowtie2db humann3_db/metaphlan_db_vJun23 -x mpa_vJun23_CHOCOPhlAnSGB_202307”

which tells me:

CRITICAL ERROR: Can not call software version for metaphlan

Would you please help me understand what I am missing?

Thanks!

Faezeh

Installing Baqlava