Recycle.py: Runtime error

[Freemacl]

When I try to execute recycle.py, I get the following error:

Traceback (most recent call last):
File "/home/imss/.local/bin/recycle.py", line 4, in
import('pkg_resources').run_script('recycler==0.62', 'recycle.py')
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 738, in run_script
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1506, in run_script
File "/home/imss/.local/lib/python2.7/site-packages/recycler-0.62-py2.7.egg/EGG-INFO/scripts/recycle.py", line 83, in

File "/home/imss/.local/lib/python2.7/site-packages/networkx-2.0b2-py2.7.egg/networkx/classes/digraph.py", line 535, in remove_nodes_from
for n in nbunch:
File "/home/imss/.local/lib/python2.7/site-packages/networkx-2.0b2-py2.7.egg/networkx/algorithms/isolate.py", line 94, in
return (n for n, d in G.degree() if d == 0)
File "/home/imss/.local/lib/python2.7/site-packages/networkx-2.0b2-py2.7.egg/networkx/classes/reportviews.py", line 367, in iter
for n in self._nodes:
RuntimeError: dictionary changed size during iteration

System: Ubuntu Linux
For what it's worth, I was able to get everything up and running on my personal comp (mac osx), but I'm hoping to use this [unfortunately problematic] computer as it is much faster.

[rozovr]

Thanks. Are you sure all the dependencies are covered? How did you install?

[Freemacl]

MacOS (works):

• numpy 1.12.1
• networkx 1.11
• pysam 0.11.2.2
• nose 1.3.7
• BWA 0.7.5a
• samtools 1.5
• SPAdes 3.10.1
  none of the dependencies were met, so I installed with conda

Ubuntu (doesn't work):

• numpy 1.11.1
• networkx 2.0b2
• pysam 0.12
• nose 1.3.7
• BWA 0.7.12
• samtools 1.5
• SPAdes 3.10.1
  Was only missing networkX, which I installed via pip

[salvoc81]

I was getting the same error on MacOS 10.12 (Sierra). Matching the versions of the module fixed the issue.

[rozovr]

Hi @salvoc81, do you mean the versions that are in the README?
@Freemacl, sorry for my delay, am wrapping up my thesis now; will look into this soon

[nwatarai]

Hi, I got the same error, but downgraded Python networkX from 2.0 to 1.11 and the error disappeared.

[Freemacl]

@nwatarai @salvoc81 Thanks for the help! That fixed my issue. Phew.

[dpellow]

I got this as well. Fixed by changing line 83 of recycle.py:
G.remove_nodes_from(nx.isolates(G)) --> G.remove_nodes_from(list(nx.isolates(G)))

See: http://pelegm-networkx.readthedocs.io/en/latest/reference/generated/networkx.algorithms.isolate.isolates.html

[dpellow]

Merged bug fix into master