Output phylogeny from [tree1] not recognized

Microbial community profiling StrainPhlAn
1 
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:

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

2

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

3

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.