You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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. Running the Conda version in a Conda environment with Python 3.8.2., I use the following command:
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
I've tried running with different files as reference or query, including running with a file of unordered contigs as my query. I've also tried running this with the --fill-only option. All yield the same error. Scaffolding works totally fine. Any ideas?
The text was updated successfully, but these errors were encountered:
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. Running the Conda version in a Conda environment with Python 3.8.2., I use the following command:
ragtag.py patch liberibacter_central_ragtag.fasta liberibacter_central_assembly.fasta
But when I attempt to run it I get the following error:
I've tried running with different files as reference or query, including running with a file of unordered contigs as my query. I've also tried running this with the --fill-only option. All yield the same error. Scaffolding works totally fine. Any ideas?
The text was updated successfully, but these errors were encountered: