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maxplanck-ie / HiCAssembler

Software to assemble contigs/scaffolds into chromosomes using Hi-C data
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ValueError: 'ScaffHiC_xxx' is not in list #18

Open yangxiaofeill opened 4 years ago

yangxiaofeill commented 4 years ago

Hi author, I tried HiCAssembler, however, there are some errors like:

Scaffolds:['ScaffHiC_424/1', 'ScaffHiC_636/2', 'ScaffHiC_424/2', 'ScaffHiC_564']
DEBUG:HiCAssembler:Removing weak edge in path connecting two hic-scaffolds: edge: ('ScaffHiC_636/2', 'ScaffHiC_424/2'), weight: 52731.08417428207
Traceback (most recent call last):
  File "~/miniconda3/envs/hicexplorer_new/bin/assemble", line 312, in <module>
    main(args)
  File "~/miniconda3/envs/hicexplorer_new/bin/assemble", line 306, in main
    super_contigs = assembl.assemble_contigs()
  File "~/miniconda3/envs/hicexplorer_new/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 210, in assemble_contigs
    self.put_back_small_scaffolds()
  File "~/miniconda3/envs/hicexplorer_new/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 728, in put_back_small_scaffolds
    idx_u = path.index(min_edge[0])
ValueError: 'ScaffHiC_636/2' is not in list

What is the solution for this error?

Best Xiaofei