Question: Using Biopython to access MUSCLE
gravatar for jtbioinfo
3.5 years ago by
New York
jtbioinfo0 wrote:

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
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')

, 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!

biopython alignment • 1.8k views
ADD COMMENTlink written 3.5 years ago by jtbioinfo0

It might be better to ask in the biopython mailing list. But it seems like the interface of muscle has changed

ADD REPLYlink written 3.5 years ago by LluĂ­s R.910

Thank you - I'll try that.

ADD REPLYlink written 3.5 years ago by jtbioinfo0
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