Metaphlan3, export2graphlan, graphlan compatibility issues


I’m experiencing compatibility issues when using MetaPhlan3 (3.0.9) input in export2graphlan (0.22). I’m not getting any error but the resulting Graphlan (1.1.3) graph is incorrect. See image below.


I’ve tried the --legacy-output option in MetaPhlan but the results remain the same.


When running export2graphlan and graphlan with the same versions and code for MetaPhlan2 output, the graph is displayed correctly. Are there any parameters that need to be set differently in conjunction with metaphlan3?

metaphlan ZR_BioPool_DNA_I_15308.fastq --bowtie2out ZR_BioPool_DNA_I_15308_bowtie.bz2 --nproc 8 --input_type fastq --bowtie2db /nfs/databases/metaphlan3/20210602/ -x mpa_v30_CHOCOPhlAn_201901 --biom ZR_BioPool_DNA_I_15308_biom.txt > ZR_BioPool_DNA_I_15308_metaphlan_profile.txt -i ZR_BioPool_DNA_I_15308_metaphlan_profile.txt --tree ZR_BioPool_DNA_I_15308.tree.txt --annotation ZR_BioPool_DNA_I_15308.annot.txt --most_abundant 100 --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 --external_annotations 7 --min_clade_size 1 --annotation_legend_font_size 8 --fname_row 3 --skip_rows 0,1,2,3 --annot ZR_BioPool_DNA_I_15308.annot.txt ZR_BioPool_DNA_I_15308.tree.txt ZR_BioPool_DNA_I_15308.xml --dpi 300 ZR_BioPool_DNA_I_15308.xml ZR_BioPool_DNA_I_15308.png

Is this a known issue?

Adding the intermediary files.
ZR_BioPool_DNA_I_15308.xml.txt (25.2 KB)

I’m experiencing a similar issue as I’ve gone through the Metaphlan3 tutorial.

When trying to install export2graphlan, I receive an UnsatisfiableError that says export2graphlan requires python 2.7. The tutorial states Metaphlan3 requires python 3 or higher, and I have installed Metaphlan3 and Humann3 within a python 3.7 environment.

Is there a process to integrate export2graphlan in a python >=3.0 environment?