# Phylophlan Discard a few mags **URL:** \ **Category:** PhyloPhlAn\ **Created:** [September 4, 2026, 5:52pm UTC](https://forum.biobakery.org/t/phylophlan-discard-a-few-mags/9053 "2026-09-04T17:52:37Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Skylady](https://avatars.discourse-cdn.com/v4/letter/s/7ab992/32.png) [@Skylady](https://forum.biobakery.org/u/Skylady)\ **Post date:** [September 4, 2026, 5:52pm UTC](https://forum.biobakery.org/t/phylophlan-discard-a-few-mags/9053/1 "2026-09-04T17:52:37Z")
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. ---
**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\ **Post date:** [September 10, 2026, 7:17am UTC](https://forum.biobakery.org/t/phylophlan-discard-a-few-mags/9053/2 "2026-09-10T07:17:40Z")
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