Phylophlan Discard a few mags

Microbial community profiling PhyloPhlAn
1

Hi!

I tried to use PhyloPhlAn version 3.2.1 (13 February 2026) for MAGs, and saw that output file don’t have two MAGs, they are totally gone I have checked in each folder of tmp.

In log file I have 152 as input files, and they gone on this step - Generate proteomes from 150 genomes, after that - Selecting 150 markers from “/home/my_mags_genomes/phylophlan_results/tmp/map_aa” … So I have a question why this could have happened?

I used script like that -

phylophlan -i /home/my_mags_genomes
-d phylophlan
–diversity high
–fast
-f supermatrix_aa.cfg
-o /home/my_mags_genomes/phylophlan_results
–genome_extension .fasta
–nproc 30
–verbose

Can I alter it somehow to get all my mags on the tree?

Thanks,

Best.

2

Dear @Skylady, thank you for using PhyloPhlAn and for reporting this. Will you be able to attache the output printed by PhyloPhlAn? I see you specified the --verbose param and that can help understand why your input MAGs were discarded. Although, if I have to guess, it could be because not enough markers were found.

Thanks,

Francesco