can someone help me make sense of this error message? Its from an IPython cell in Beaker Notebook, running T-cofee in command line through biopython.
Non-zero return code 11 from 't_coffee -output clustalw -infile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/uniprot-ornithine+transcarbamylase-2.fasta -outfile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/aligned.aln', message 'PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 21:55:14 - Revision 8cbe486 - Build 470)'
Non-zero return code 11 from 't_coffee -output clustalw -infile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/uniprot-ornithine+transcarbamylase-2.fasta -outfile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/aligned.aln', message 'PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 21:55:14 - Revision 8cbe486 - Build 470)'
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ApplicationError Traceback (most recent call last)
<ipython-input-1-5970d9b8d2e2> in <module>()
97 tcoffee_cline = TCoffeeCommandline(infile="/Applications/Beaker.app/Contents/Resources/dist/src/main/web/%s"%(fName2), output="clustalw", outfile="/Applications/Beaker.app/Contents/Resources/dist/src/main/web/aligned.aln")
98 #executes command line wrapper
---> 99 tcoffee_cline()
100 #read in the alignment file
101 alignment = AlignIO.read(open("/Applications/Beaker.app/Contents/Resources/dist/src/main/web/aligned.aln"), "clustal")
//anaconda/lib/python2.7/site-packages/Bio/Application/__init__.pyc in __call__(self, stdin, stdout, stderr, cwd, env)
513 if return_code:
514 raise ApplicationError(return_code, str(self),
--> 515 stdout_str, stderr_str)
516 return stdout_str, stderr_str
517
ApplicationError: Non-zero return code 11 from 't_coffee -output clustalw -infile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/uniprot-ornithine+transcarbamylase-2.fasta -outfile /Applications/Beaker.app/Contents/Resources/dist/src/main/web/aligned.aln', message 'PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 21:55:14 - Revision 8cbe486 - Build 470)'
Happy to answer any questions if it will help. Thanks!