RagTag patch error--"tuple index out of range"

Question

[schmiggle]

I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching long-read sections. The RagTag "patch" function, if I understand correctly, is supposed to do exactly this. I use this command:

ragtag.py patch liberibacter_central_ragtag.fasta liberibacter_central_assembly.fasta

But when I attempt to run it I get the following error:

Traceback (most recent call last):
File "/home/u30/moshesteyn/.conda/envs/py382/bin/ragtag_patch.py", line 518, in <module>
    main()
File "/home/u30/moshesteyn/.conda/envs/py382/bin/ragtag_patch.py", line 497, in main
    match_psg = aln_psg.max_weight_matching()
File "/home/u30/moshesteyn/.conda/envs/py382/lib/python3.8/site-packages/ragtag_utilities/ScaffoldGraph.py", line 824, in max_weight_matching
    for cc in nx.connected_components(G=cover_graph):
File "/home/u30/moshesteyn/.conda/envs/py382/lib/python3.8/site-packages/networkx/classes/backends.py", line 134, in wrapper
    graph = args[0]
IndexError: tuple index out of range

Does anyone know what might be causing this error? No one else seems to have run into it on the github. I've run it with both files individually against a known reference, as well as reversing the order of the files, and I have the same problem.

Answer 1

[Ming]

I had the same error when i used ragtag v2.0.1. After updating ragtag to v2.1.0, I can run successfully