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After correcting the HiC matrix I run into this problem that was already mentioned by other users. I was wondering if you have found a solution.
Cheers!
WARNING:Scaffolds:
Hub-hub contact for bin_id:583 scaffold: ctg002710_np12_7 degree: 4
with bin_id: 1958 scaffold: ctg002520_np12_7 degree:4
##############
these cases could introduce problems in the assembly.
Thus, node is being removed from the graph.
##############
Traceback (most recent call last):
File "/usr/local/bin/assemble", line 312, in
main(args)
File "/usr/local/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/usr/local/lib/python3.8/dist-packages/hicassembler/HiCAssembler.py", line 200, in assemble_contigs
self.scaffolds_graph.join_paths_max_span_tree(conf_score, node_degree_threshold=2e3,
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 1814, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 2013, in _remove_weakest
if len(path) < 5:
TypeError: object of type 'int' has no len()
The text was updated successfully, but these errors were encountered:
Hello,
After correcting the HiC matrix I run into this problem that was already mentioned by other users. I was wondering if you have found a solution.
Cheers!
WARNING:Scaffolds:
Hub-hub contact for bin_id:583 scaffold: ctg002710_np12_7 degree: 4
with bin_id: 1958 scaffold: ctg002520_np12_7 degree:4
##############
these cases could introduce problems in the assembly.
Thus, node is being removed from the graph.
##############
Traceback (most recent call last):
File "/usr/local/bin/assemble", line 312, in
main(args)
File "/usr/local/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/usr/local/lib/python3.8/dist-packages/hicassembler/HiCAssembler.py", line 200, in assemble_contigs
self.scaffolds_graph.join_paths_max_span_tree(conf_score, node_degree_threshold=2e3,
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 1814, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/usr/local/lib/python3.8/dist-packages/hicassembler/Scaffolds.py", line 2013, in _remove_weakest
if len(path) < 5:
TypeError: object of type 'int' has no len()
The text was updated successfully, but these errors were encountered: