TypeError: object of type 'int' has no len()

[xinwang-bio]

Hi
When I used this tool, I got an error as below. How can I fix it ?

Thanks

Hub-hub contact for bin_id:30767 scaffold: tig00000201_arrow_pilon/5_0 degree: 8
with bin_id: 30766 scaffold: tig00000201_arrow_pilon/4_58 degree:23

##############
these cases could introduce problems in the assembly.
Thus, node is being removed from the graph.
##############

Traceback (most recent call last):
File "/home/xinwang/local/miniconda2/bin/assemble", line 312, in
main(args)
File "/home/xinwang/local/miniconda2/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
hub_solving_method='remove weakest')
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1803, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/home/xinwang/local/miniconda2/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()

[fidelram]

do you have the latest version of HiCExplorer? The .h5 matrix that you are trying to load does not have some information, namely 'correction_factors`

…

On Sun, Mar 3, 2019 at 4:33 AM Xin Wang ***@***.***> wrote: Hi When I used this tool, I got an error as below. How can I fix it ? Thanks INFO:HiCAssembler:Using previously computed scores: Pimp_10kb_corrected/misassembly_score.txt Pimp_10kb_corrected/zscore_matrix.h5 Traceback (most recent call last): File "/home/xinwang/local/miniconda2/bin/assemble", line 312, in main(args) File "/home/xinwang/local/miniconda2/bin/assemble", line 304, in main scaffolds_to_ignore=args.scaffolds_to_ignore) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 88, in *init* self.load_hic_matrix(hic_file_name, split_misassemblies, split_positions_file, matrix_bin_size) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 141, in load_hic_matrix self.split_misassemblies(hic_file_name, split_positions_file) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 857, in split_misassemblies ft.hic_ma = HiCMatrix.hiCMatrix(zscore_matrix_file) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py", line 85, in *init* hiCMatrix.load_h5(matrixFile) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py", line 288, in load_h5 distance_counts = f.root.correction_factors.read() File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/tables/group.py", line 840, in *getattr* return self._f_get_child(name) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/tables/group.py", line 712, in _f_get_child self._g_check_has_child(childname) File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/tables/group.py", line 399, in _g_check_has_child % (self._v_pathname, name)) tables.exceptions.NoSuchNodeError: group / does not have a child named correction_factors — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEu_1TyBHk_fG7CZSihwVs7C0cX3aDggks5vS0KkgaJpZM4baw7X> .

[xinwang-bio]

@fidelram
Now. I faced another problem like below.
Hub-hub contact for bin_id:30767 scaffold: tig00000201_arrow_pilon/5_0 degree: 8
with bin_id: 30766 scaffold: tig00000201_arrow_pilon/4_58 degree:23

##############
these cases could introduce problems in the assembly.
Thus, node is being removed from the graph.
##############

Traceback (most recent call last):
File "/home/xinwang/local/miniconda2/bin/assemble", line 312, in
main(args)
File "/home/xinwang/local/miniconda2/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
hub_solving_method='remove weakest')
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/home/xinwang/local/miniconda2/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1803, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/home/xinwang/local/miniconda2/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()

[Karimi-81]

Hi There,
I also encountered with the same issue:
WARNING:Scaffolds:

Hub-hub contact for bin_id:9590 scaffold: ptg000031l/8_0 degree: 3
with bin_id: 9921 scaffold: ptg000031l/25_116 degree:4

##############
these cases could introduce problems in the assembly.
Thus, node is being removed from the graph.
##############

Traceback (most recent call last):
File "/home/karimi81/env_HiCAssembler_p27/bin/assemble", line 312, in
main(args)
File "/home/karimi81/env_HiCAssembler_p27/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/home/karimi81/env_HiCAssembler_p27/lib/python2.7/site-packages/hicassembler/HiCAssembler.py", line 201, in assemble_contigs
hub_solving_method='remove weakest')
File "/home/karimi81/env_HiCAssembler_p27/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 27, in wrapper
f_result = func(*args, **kwds)
File "/home/karimi81/env_HiCAssembler_p27/lib/python2.7/site-packages/hicassembler/Scaffolds.py", line 1803, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/home/karimi81/env_HiCAssembler_p27/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()

Did you solve this problem. Can you please guide me to solve it.

[grpiccoli]

I am having the same issue, has anyone solved it?