Open gtrichard opened 5 years ago
Looks like a corner condition was reached and the code was not prepared to handle it. Path, in this case is a list of id, that define continuity of a sequence. It should not be an integer. I would need some sample data to debug that.
Ok, so path = len(self.pg_base[node])
should definitely be path = self.pg_base[node]
?
Corner would mean what? The following?
---o---------o
/ \
/ \
o-----o-----o-----o-----o-----o-----o
Any idea about the cause of this?
For the sample data you would need the whole h5 matrix + fasta?
Thanks a bunch for the answer.
@gtrichard Hi I also face this error. How you can fix it ?
I got the same error.
`INFO:Scaffolds:Entering join_paths_max_span_tree /public1/home/ruifeng/anaconda3/envs/hicexplorer/lib/python3.6/site-packages/scipy/sparse/compressed.py:742: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient. SparseEfficiencyWarning) INFO:Scaffolds:320 hubs were found WARNING:Scaffolds:
Hub-hub contact for bin_id:20481 scaffold: scaffold_177_1 degree: 4 with bin_id: 20358 scaffold: scaffold_115/2_2 degree:4
############## these cases could introduce problems in the assembly. Thus, node is being removed from the graph. ##############
Traceback (most recent call last):
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/bin/assemble", line 312, in
Hi @gtrichard @wangxinbio, how did you solve it?
Hi @fidelram, is there any software update regarding this error?
Thanks!
I didn't solve it.
Has someone solved this issue?
@gtrichard you did solve it in the end, thank you for the comment, that was the solution, cheers
One of my former colleague is trying to use HiCAssembler. He launched the following command:
And received this error:
When checking the code of Scaffolds.py, between lines 1997 and 2006, I saw that
path
is defined as the length of something, so it is an integer that of course doesn't have a length itself soif len(path) < 5:
is crashing.I told him to replace line 1999 of Scaffolds.py
path = len(self.pg_base[node])
bypath = self.pg_base[node]
. Then he received a different error:He installed HiCAssembler and HiCExplorer with the following commands: