I’m using phylophlan_metagenomic to classify my metagenome bins, however the resulting .tsv file is telling me that all of the bins have been identified as the same species.
Initially I used Prodigal to convert my .fa files from metabat to .faa files and used the SGB,Jul20 database. This identified every bin as:
uSGB_39697:Other:k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB7364|o__OFGB7364|f__FGB7364|g__GGB27422|s__GGB27422_SGB39697|t__SGB39697:1.0
I then copied over all the .faa files generated by CheckM and used the SGB.Jan19 database. This identified every bin as:
uSGB_5750:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__GGB4250|s__GGB4250_SGB5750|t__SGB5750:1.0
I’m at a complete loss for what to do next! My code is:
phylophlan_metagenomic --nproc 120
-i <input directory of .faa files>
-d SGB.Jan19
-n 1
-o