Disentangling failed

[leogg-github]

Hi,

I have seen a couple of threads with a similar problem, but I fail to see what is the problem... For a result that gave me no warnings the graph seems to still show some connections with mitochondrial segments, while the one that says "disentangling failed" seems more complex but I still do not clearly see the difference from the two graphs in terms of why the second one failed. Is there a way to know what nodes were selected to build the assembly from the graph?

extended_K115.assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv
get_org.log.txt

extended_K115.assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv
get_org.log.txt

Any help would be appreciated.

Thank you

[Kinggerm]

Please update the graph with name, depth, length shown in Bandage.
As I can tell from the connection and the relative coverages, these two graphs are both organelle-sufficient.

[leogg-github]

Here are the updated graphs. The first one was organelle sufficient according to the log, but if you check the second log you will see the issues on this case. I have already tried reducing the word size but that resulted in more potential assemblies.

Thanks for your help

[leogg-github]

I just also ran using a closely related genome (using -s) and got a 6 different assemblies with 3 scaffolds each. This seems odd since I would expect a consistent assembly if I use the same species as target.

Funnily enough the second graph which corresponded to the initial run I performed with default parameters did provide a single scaffold, but my doubt remains... why is the log presenting disentangling failures?

Thanks