<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hello,<div><br></div><div>I am trying to run alignment using ClustalW in python.</div><div><br></div><div>I have used this code to compile</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><blockquote type="cite"><div>cline = ClustalwCommandline("clustalw2", infile="test.fasta")</div><div>print(cline)</div><div>stdout, stderr = cline()</div><div>align = AlignIO.read("test.aln", "clustal")</div><div>print(align)</div></blockquote><br></blockquote>But it is generating file. I think I have some problem with setting a proper pathway to clustal.<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"></blockquote><div><br></div><div>This is the error:</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><blockquote type="cite"><div>clustalw2 -infile=test.fasta</div><div>Traceback (most recent call last):</div><div> File "/Users/user/Google Drive/Bioinformatics/smallRNAseq/Python U densities/trial4old.py", line 95, in <module></div><div> stdout, stderr = cline()</div><div> File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/Bio/Application/__init__.py", line 513, in __call__</div><div> stdout_str, stderr_str)</div><div>Bio.Application.ApplicationError: Non-zero return code 127 from 'clustalw2 -infile=test.fasta', message '/bin/sh: clustalw2: command not found'<span></span></div></blockquote></blockquote><div><br></div><div><br></div><div>Can you suggest some solution?</div><div><br></div><div>Thanks,</div><div><br></div><div>Jakub</div><div><br></div><div><br></div></body></html>