StefanoLonardi
commented
3 years ago I was able to fix the code. First the --fasta file is required, it is the assembly that you are trying to scaffold.
Regarding the code, according to
https://networkx.org/documentation/networkx-2.3/release/release_2.0.html
G.node has been replaced by G.nodes in the new version of networkx
I had to manually change all G.node to G.nodes in HiCAssembler.py and Scaffolds.py
Finally, the function nx.connected_component_subgraphs is not available anymore, but
it can be replaced by this function that needs to be included in both HiCAssembler.py and Scaffolds.py
def connected_component_subgraphs(G):
for c in nx.connected_components(G):
yield G.subgraph(c)After all these changes, the code worked for me. It did not generate a good assembly though.
Hi there,
Could anyone shed some light on any potential issues that might result in 'assemble' crashing with the following error stack:
DEBUG:HiCAssembler:iteration: 0 N50: 8,770,000 DEBUG:HiCAssembler:Merging small bins in larger bins of size 100316 bp INFO:hicexplorer.iterativeCorrection:starting iterative correction INFO:Scaffolds:Computing stats per distance DEBUG:HiCAssembler:Confidence score set to 1499.885908354667 INFO:Scaffolds:Entering join_paths_max_span_tree INFO:Scaffolds:190 hubs were found Traceback (most recent call last): File "./HiCAssembler/bin/assemble", line 312, in
main(args)
File "./HiCAssembler/bin/assemble", line 306, in main
super_contigs = assembl.assemble_contigs()
File "/homes/lcampbell/hps_nobackup2_lcampbell/Software/miniconda2/lib/python3.7/site-packages/hicassembler/HiCAssembler.py", line 202, in assemble_contigs
hub_solving_method='remove weakest')
File "/homes/lcampbell/hps_nobackup2_lcampbell/Software/miniconda2/lib/python3.7/site-packages/hicassembler/Scaffolds.py", line 28, in wrapper
f_result = func(*args, **kwds)
File "/homes/lcampbell/hps_nobackup2_lcampbell/Software/miniconda2/lib/python3.7/site-packages/hicassembler/Scaffolds.py", line 1815, in join_paths_max_span_tree
self._remove_weakest(nxG)
File "/homes/lcampbell/hps_nobackup2_lcampbell/Software/miniconda2/lib/python3.7/site-packages/hicassembler/Scaffolds.py", line 1966, in _remove_weakest
node_degree_mst = dict(G.degree(G.node.keys()))
AttributeError: 'Graph' object has no attribute 'node'
HiCAssembler was installed on our cluster by using the following approach:
git checkout -b 2to3 --track origin/2to3 And editing the setup.py, by commenting out the line: "#package_data={'': '*.txt'},"
I figured if I could at least run the example data, that might shed some light. BUT NO....
In addition, how is it possible to run even the test data through assemble ? If assemble complains it has not been provided with a fasta, of which I can not locate any associated fasta file for the example data 'hic_small.h5'.
Proposed command to run example data: "assemble -m Hi_C_matrix_corrected.h5 -o ./assembly_output \ --min_scaffold_length 100000 --bin_size 5000 --misassembly_zscore_threshold -1.0 \ --num_iterations 3 --num_processors 16"
Results of running the above give the error: assemble: error: the following arguments are required: --fasta/-f !
What gives ? Is the fasta file, an output file to capture scaffolded assembly, or input of the original assembly TO BE scaffolded. Its not entirely clear in the help documentation.