MetaPhlan doesn't detect any microbial samples

Microbial community profiling MetaPhlAn
1

Hi!

I have a problem with MetaPhlAn version 4.1.1 (11 Mar 2024) with database mpa_vOct22_CHOCOPhlAnSGB_202403. MetaPhlAn show me communicat:

WARNING: MetaPhlAn did not detect any microbial taxa in the sample.

It was a sample from some paper, so I know it has to contain bacterial sequences. To confirm this I ran Kraken2 on this data and it showed 98% of bacterial DNA.

What is a problem? How can I handle it?

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image
image998×594 14.5 KB

This is a fragment of .bowtie2 temporally file. It contains 1000 lines from 31 000 reads

3

Hi @Daniel_Pysz

Are you sure the sample is obtained through shotgun metagenomic sampling? By looking up the sample id it seems like this is was amplicon sequenced. MetaPhlAn works only on metagenomes.