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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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errors when running the test-SuperPang.py #9

Closed liushanlin closed 1 year ago

liushanlin commented 1 year ago

the error message is as follows:

Reconstructing contigs File "/home/sl/.conda/envs/SuperPang/bin/condense-edges.py", line 254, in main() File "/home/sl/.conda/envs/SuperPang/bin/condense-edges.py", line 60, in main GS.add_edge_list(edges) File "/home/sl/.conda/envs/SuperPang/lib/python3.8/site-packages/graph_tool/init.py", line 2603, in add_edge_list libcore.add_edge_list_iter(self.__graph, edge_list, eprops) TypeError: No registered converter was able to produce a C++ rvalue of type double from this Python object of type Vertex

There was an error running condense-edges.py.

fpusan commented 1 year ago

Thanks for trying SuperPang May I ask what is your operating system and distribution? Did the first part of the pipeline (before condense edges) run correctly?

fpusan commented 1 year ago

Nevermind, could reproduce the issue in my computer.

Turns out that they released a new update of graph-tool in anaconda cloud yesterday, and it somehow breaks that piece of code. For now, you can revert to the old graph-tool version by typing conda install -c conda-forge graph-tool=2.45 when inside your SuperPang environment. This fixed the issue for me.

Tomorrow I will work on a more permanent solution and make a new release when get everything sorted out.

Thanks for reporting!

liushanlin commented 1 year ago

It works. Thanks for the quick reply.

fpusan commented 1 year ago

I just released a new version including a fix for the issue