Inputting data into phylophlan_metagenomic

Microbial community profiling PhyloPhlAn
1

I have a set of assemblies for the genus Bacteroides but when I run phylophlan_metagenomic to create bins for these assemblies I am unable to run it without it crashing and not loading.

The command I am using is

phylophlan_metagenomic \
-i NCBI_Bacteroides_assembly_proteins
–nproc 4
-n 1
-d SGB.Jan19

Is there a way to speed up the process or would reducing the input in the assembly protein folder be the only way to make this process quicker? Thanks in advance

2

Hi there, and apologies for the late reply.
I’m not sure I got your question right:

phylophlan_metagenomic do not bin assembled contigs but instead assigns the user’s input genomes/MAGs to existing species-level genome bins (SGBs).

Would be helpful in this case to better understand the content of the input folder NCBI_Bacteroides_assembly_proteins and also if you can provide the log/error that phylophlan_metagenomic produces.

Many thanks,
Francesco