Infinite recursion in clean.py ?

[aWormGuy]

Hi,
I installed circlator version 1.5.2 via bioconda, tried running the entire circlator pipeline using:

circlator all $POLISHED_ASSEMBLY $PRE_ASSEMBLED_READS $OUTPUT_DIR;

I am getting the following error:

Traceback (most recent call last):
File "/myhomefolder/anaconda3/lib/python3.6/site-packages/circlator/clean.py", line 145, in _get_all_containing
new_names = self._get_all_containing(containing_contigs, containing_contig, exclude=name)
File "/myhomefolder/anaconda3/lib/python3.6/site-packages/circlator/clean.py", line 145, in _get_all_containing
new_names = self._get_all_containing(containing_contigs, containing_contig, exclude=name)
File "/myhomefolder/anaconda3/lib/python3.6/site-packages/circlator/clean.py", line 145, in _get_all_containing
new_names = self._get_all_containing(containing_contigs, containing_contig, exclude=name) [Previous line repeated 995 more times]
File "/myhomefolder/anaconda3/lib/python3.6/site-packages/circlator/clean.py", line 138, in _get_all_containing
contains_name = set()
RecursionError: maximum recursion depth exceeded while calling a Python object

I get the same error even after I tried increasing the recursion depth using the following :

import sys
sys.setrecursionlimit(10000)

Any tips on how to avoid this?

Thanks,
-Amit.

[andrewjpage]

I've updated the code to fix this bug. Please update to version 1.5.5. Thanks for reporting it.