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fpusan / SuperPang

Non-redundant pangenome assemblies from multiple genomes or bins
BSD 3-Clause "New" or "Revised" License
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ValueError: invalid vertex: 3; condense-edges.py error. #13

Closed pavlohrab closed 5 months ago

pavlohrab commented 6 months ago

Hi,

I was trying to run Superpang on a 50 MAGs (supposedly 1 species) . It returned the following error:

Traceback (most recent call last):
  File "/lustre/BIF/nobackup/hrab001/micromamba/envs/superpang/lib/python3.8/site-packages/superpang/scripts/condense-edges.py", line 278, in <module>
    main(parse_args())
  File "/lustre/BIF/nobackup/hrab001/micromamba/envs/superpang/lib/python3.8/site-packages/superpang/scripts/condense-edges.py", line 222, in main
    predecessors, successors = G2dicts(GS, name2vertex, vertex2name)
  File "/lustre/BIF/nobackup/hrab001/micromamba/envs/superpang/lib/python3.8/site-packages/superpang/scripts/condense-edges.py", line 238, in G2dicts
    for pv in GS.get_in_neighbors(v):
  File "/lustre/BIF/nobackup/hrab001/micromamba/envs/superpang/lib/python3.8/site-packages/graph_tool/__init__.py", line 2441, in get_in_neighbors
    vertices = libcore.get_in_neighbors_list(self.__graph, int(v),
ValueError: invalid vertex: 3

There was an error running condense-edges.py. Please open an issue

Can you advice on resolving it?

Best, Pavlo

fpusan commented 6 months ago

Is this happening with the latest version of SuperPang? Can you share those 50 genomes with me so I can try to replicate?

fpusan commented 5 months ago

Managed to reproduce this. mamba install -c conda-forge graph-tool==2.45 will fix the bug for you. I will try to find a more proper fix and release a patch ASAP

fpusan commented 5 months ago

I just released version 1.3.0.post1, which adds compatibility with newer graph-tool versions.