# Output phylogeny from \[tree1\] not recognized

**URL:** <https://forum.biobakery.org/t/output-phylogeny-from-tree1-not-recognized/1652>\
**Category:** StrainPhlAn\
**Created:** [February 5, 2021, 1:01pm UTC](https://forum.biobakery.org/t/output-phylogeny-from-tree1-not-recognized/1652 "2021-02-05T13:01:32Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [February 5, 2021, 1:01pm UTC](https://forum.biobakery.org/t/output-phylogeny-from-tree1-not-recognized/1652/1 "2021-02-05T13:01:32Z")

</div>

```auto
phylophlan_write_config_file --db_dna makeblastdb --map_dna blastn --msa mafft --trim trimal --tree1 raxml --tree2 raxml -d n -o sp3/ph3.config --overwrite

strainphlan --phylophlan_mode accurate --marker_in_n_samples 80 --sample_with_n_markers 20 \
  --nproc 8 -s sp3/consensus_markers/*.pkl \
  -m sp3/db_markers/s__Faecalibacterium_prausnitzii.fna \
  -d $DBDIR -c s__Faecalibacterium_prausnitzii -o sp3_out \
  --phylophlan_configuration sp3/ph3.config

```

Output:

```auto
Fri Feb 5 13:56:22 2021: Start StrainPhlAn 3.0 execution
Fri Feb 5 13:56:22 2021: Creating temporary directory...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Getting markers from main sample files...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Getting markers from main reference files...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Removing bad markers / samples...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Writing samples as markers' FASTA files...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Writing filtered clade markers as FASTA file...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Calculating polymorphic rates...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Executing PhyloPhlAn 3.0...
Fri Feb 5 13:56:22 2021: Creating PhyloPhlAn 3.0 database...
Fri Feb 5 13:56:22 2021: Done.
Fri Feb 5 13:56:22 2021: Processing samples...[e] "/ebio/abt3_projects/software/dev/ll_pipelines/llmgps/.snakemake/conda/5e96ed0a/lib/python3.8/site-packages/phylophlan/phylophlan_configs/" folder does not exists
[e] output phylogeny from [tree1] not recognized

[e] An error was ocurred executing a external tool, exiting...
Fri Feb 5 13:56:27 2021: Stop StrainPhlAn 3.0 execution.

```

If I don’t provide the config file, then strainphlan3 completes successfully. I’m running `metaphlan 3.0.7 bioconda`

---

<div class="post-metadata">

**Author:** ![nick-youngblut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nick-youngblut/32/528_2.png) [@nick-youngblut](https://forum.biobakery.org/u/nick-youngblut)\
**Post date:** [February 5, 2021, 2:15pm UTC](https://forum.biobakery.org/t/output-phylogeny-from-tree1-not-recognized/1652/2 "2021-02-05T14:15:41Z")

</div>

This error appears to be a result of including `[tree2]` in the config. Removing this section from the config results in strainphlan completing successfully

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [February 8, 2021, 9:44am UTC](https://forum.biobakery.org/t/output-phylogeny-from-tree1-not-recognized/1652/3 "2021-02-08T09:44:05Z")

</div>

Hi @nick-youngblut  
The PhyloPhlAn `tree2` parameter was thought for refining with raxml the phylogeny built by the `tree1` (for example a phylogeny built by fasttree) In your case, PhyloPhlAn is failing because you already use as `tree1` raxml.