Hello! I am very new to computing and have run into an issue I cannot seem to find a solution for online. I am trying to use the Biopython wrapper to access MUSCLE in order to align ~100 sequences of 5-10kb. I believe I have successfully installed MUSCLE - when I type muscle into my command line, I get the following:
MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. Basic usage muscle -in <inputfile> -out <outputfile> Common options (for a complete list please see the User Guide): -in <inputfile> Input file in FASTA format (default stdin) -out <outputfile> Output alignment in FASTA format (default stdout) -diags Find diagonals (faster for similar sequences) -maxiters <n> Maximum number of iterations (integer, default 16) -maxhours <h> Maximum time to iterate in hours (default no limit) -html Write output in HTML format (default FASTA) -msf Write output in GCG MSF format (default FASTA) -clw Write output in CLUSTALW format (default FASTA) -clwstrict As -clw, with 'CLUSTAL W (1.81)' header -log[a] <logfile> Log to file (append if -loga, overwrite if -log) -quiet Do not write progress messages to stderr -version Display version information and exit Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2 Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3 Fastest possible (nucleotides): -maxiters 1 -diags
However, when I attempt to use the Biopython wrapper in my IDE just as in the example from the Biopython tutorial:
from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input='opuntia.fasta') cline()
, I get the following error:
Bio.Application.ApplicationError: Non-zero return code 2 from '<file_name>' message 'MUSCLE v3.8.31 by Robert C. Edgar'
Does anybody have any idea as to what could be causing the error?
Thanks in advance!