When I try to run the FastTree wrapper from Bio.Phylo.Applications, it fails, giving me this message:
ApplicationError: Non-zero return code 1 from '/home/fetz/genome/phylosift_v1.0.1/bin/FastTree -nt -gtr -out 245_hypothetical_protein.tre 245_hypothetical_protein.codon', message 'Unknown or incorrect use of option -out'
My Biopython version is 1.68:
import Bio Bio.__version__ '1.68'
My code, run in ipython3, is:
from Bio.Phylo.Applications import _Fasttree fasttree_exe = r"/home/fetz/genome/phylosift_v1.0.1/bin/FastTree" codonfile = "245_hypothetical_protein.codon" outfile = codonfile.replace(".codon",".tre") cmd = _Fasttree.FastTreeCommandline(fasttree_exe, nt = True, gtr = True, input = codonfile, out = outfile) cmd()
The input file, 'codonfile,' is a verified codon alignment from the Bio.codonalign module that has been written to a file. I cannot find any errors in my command construction according to the example given in the API. Can anyone suggest what I am doing wrong? Thank you in advance.