object of type 'int' has no len() in Scaffolds.py _remove_weakest len(path)

[gtrichard]

One of my former colleague is trying to use HiCAssembler. He launched the following command:

assemble -m hic_corrected.h5 -o ./assembly_output  --min_scaffold_length 10000 --bin_size 5000 --misassembly_zscore_threshold -1.0  --num_iterations 3 --num_processors 16 --fasta assembly.fa

And received this error:

Traceback (most recent call last):
  File "/groups/bipaa/env/HiCExplorer_2.1.4/bin/assemble", line 312, in <module>
    main(args)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/bin/assemble", line 306, in main
    super_contigs = assembl.assemble_contigs()
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
    hub_solving_method='remove weakest')
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
    f_result = func(*args, **kwds)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1803, in join_paths_max_span_tree
    self._remove_weakest(nxG)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 2002, in _remove_weakest
    if len(path) < 5:
TypeError: object of type 'int' has no len()

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 so if len(path) < 5: is crashing.

                        # adj node is hub. In this case remove the node and the scaffold it belongs
                        # to from the graph
                        path  = len(self.pg_base[node])
                        # only remove if the path is not longer than 5. Otherwise
                        # a quite large scaffold can be removed.
                        if len(path) < 5:
                            for node_id in path:
                                G.remove_node(node_id)
                            self._remove_bin_path(self.pg_base.node[node]['initial_path'], split_scaffolds=True)
                            continue

I told him to replace line 1999 of Scaffolds.py path = len(self.pg_base[node]) by path = self.pg_base[node] . Then he received a different error:

Traceback (most recent call last):
  File "/groups/bipaa/env/HiCExplorer_2.1.4/bin/assemble", line 312, in <module>
    main(args)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/bin/assemble", line 306, in main
    super_contigs = assembl.assemble_contigs()
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
    hub_solving_method='remove weakest')
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
    f_result = func(*args, **kwds)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1803, in join_paths_max_span_tree
    self._remove_weakest(nxG)
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1968, in _remove_weakest
    adj_degree = sorted([(x, node_degree_mst[x]) for x in G.adj[node].keys()], key=lambda(k, v): v)[::-1]
  File "/groups/bipaa/env/HiCExplorer_2.1.4/lib/python2.7/site-packages/networkx/classes/coreviews.py", line 81, in __getitem__
    return AtlasView(self._atlas[name])
KeyError: 19322

He installed HiCAssembler and HiCExplorer with the following commands:

conda create -p /groups/bipaa/env/HiCExplorer_2.1.4 HiCExplorer=2.1.4 biopython=1.73 python=2.7
source activate /groups/bipaa/env/HiCExplorer_2.1.4
pip install hicassembler

[fidelram]

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.

[gtrichard]

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.

[xinwang-bio]

@gtrichard Hi I also face this error. How you can fix it ?

[xuxiaoman0212]

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
main(args)
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
hub_solving_method='remove weakest')
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/lib/python3.6/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/lib/python3.6/site-packages/hicassembler/Scaffolds.py", line 1814, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/public1/home/ruifeng/anaconda3/envs/hicexplorer/lib/python3.6/site-packages/hicassembler/Scaffolds.py", line 2013, in _remove_weakest
if len(path) < 5:
TypeError: object of type 'int' has no len()
`

Hi @gtrichard @wangxinbio, how did you solve it?

Hi @fidelram, is there any software update regarding this error?

Thanks!

[gtrichard]

I didn't solve it.

[grpiccoli]

Has someone solved this issue?

[grpiccoli]

@gtrichard you did solve it in the end, thank you for the comment, that was the solution, cheers