Metaphlan3, export2graphlan, graphlan compatibility issues

Microbial community profiling MetaPhlAn
1

Hello,

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.

ZR_BioPool_DNA_I_15308
ZR_BioPool_DNA_I_153082282×2279 515 KB

ZR_BioPool_DNA_I_15308_metaphlan_profile.txt

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

ZR_BioPool_DNA_I_15308
ZR_BioPool_DNA_I_153082282×2279 517 KB

ZR_BioPool_DNA_I_15308_metaphlan_profile.txt

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

export2graphlan.py -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

graphlan_annotate.py --annot ZR_BioPool_DNA_I_15308.annot.txt ZR_BioPool_DNA_I_15308.tree.txt ZR_BioPool_DNA_I_15308.xml
graphlan.py --dpi 300 ZR_BioPool_DNA_I_15308.xml ZR_BioPool_DNA_I_15308.png

Is this a known issue?

2

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

3

Hello,
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?