Building Phylogenetic Tree - [e] gene_markers_selection crashed

I am trying to build a phylogenetic tree following Tutorial 2: Prokaryotes Tree of life reconstruction. I am using all reference genomes (17,000+) as well as 3600 of my own MAGs. See attached my output file.

Phylophlan_Output.txt (1.6 MB)

I am getting the following error:
[e] expected str, bytes or os.PathLike object, not NoneType
[e] gene_markers_selection crashed

The command I am using is:
nohup phylophlan
-i Phylophlan/Reference_Genomes
-d phylophlan
–databases_folder Phylophlan/Database
-f Phylophlan/02_tol.cfg
–diversity high
-o Phylophlan/Output
–nproc 20
–verbose 2>&1 | tee logs/phylophlan.log > Phylophlan_Output &

Help is greatly appreciated.

Kind regards,


Hi Peter, apologies for this error but I don’t have a clear answer at the moment.
I would like to ask you if you can retrieve the latest PhyloPhlAn version present in the Github repository and re-run your command above. This will help me debug this problem more easily.

Thanks a lot,

No problem.
In the end I am not sure what the exact problem was.
I re-ran the command from scratch and this time it worked without problem. Thanks for reply.

Kind regards,