Recycle.py: Runtime error

[shamir-lab]

Recycle.py: Runtime error

[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

[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]

Merged bug fix into master