Hi,
I'm using reveal realign with muscle to realign bubbles in a graph.
reveal realign --64 --method muscle --all --maxsize 5000 -o $output $input
At some point during the realignment it fails:
10/03/2018 01:04:06 PM Realigning bubble between <431323> and <99201>, 2 alleles, with muscle (max size 10bp, in nodes=2). Traceback (most recent call last): File "/ebio/abt6_projects9/abt6_software/bin/reveal/env/bin/reveal", line 11, in <module> load_entry_point('reveal==0.1', 'console_scripts', 'reveal')() File "build/bdist.linux-x86_64/egg/reveal/reveal.py", line 294, in main File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 44, in refine_bubble_cmd File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 413, in refine_all File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 206, in refine_bubble File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 483, in msa2graph AttributeError: 'exceptions.OSError' object has no attribute 'output'

I've observed this behavior in different graphs with different maxsizes. and I'm not sure how this happens.

Cheers,
Christian