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TypeError: object of type 'int' has no len() #10
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/
does not have a child named correction_factors
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
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|
@fidelram ############## Traceback (most recent call last): |
Hi There, Hub-hub contact for bin_id:9590 scaffold: ptg000031l/8_0 degree: 3 ############## Traceback (most recent call last): Did you solve this problem. Can you please guide me to solve it. |
I am having the same issue, has anyone solved it? |
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()
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