Open SethMusker opened 1 year ago
Hi Seth,
Thanks for providing enough details about this complex situation.
187292
and 189390
, upon which a consensus can be made if possible (GetOrganelle did it correctly for 187292
and 189390
), or multiple different results containing different SNPs respectively can be generated, or a single result with the highest depth. Thus, the single-component assumption can persist.188784
, 189490
, 189444
, 186851
, and 188912
together form a structure composing two pt variants with IR boundary differences. This is the real problem that triggers the failure of disentanglement. We may leave this issue open until there is a neat solution.In summary, you are right about manually removing a contig from the graph and then rerunning. However, the focal contigs are not 187292
and 189390
(you may remove one of them if you think the consensus is not a good idea though). Instead, the real solution is to remove either 189444
or 186851
.
Best, Jianjun
Hi Jianjun,
Immense thanks! Your reply was really informative and helpful. After removing 189444
the assembly finished nicely. For the record, the log is attached.
All the best, Seth
Hi,
I've had generally good success assembling chloroplasts with
get_organelle_from_assembly.py
!One of my samples fails though, with three repeats of the message
Consensus made: (187292-|189390+)
followed byDisentangling failed: 'Unable to generate result with single copy vertex percentage < 50%'
.Is this intended behaviour? I imagine that after the consensus is made, disentangling would be attempted again with the consensus sequence replacing the two previously merged edges, but this is not happening. These two edges have the same length and similar depth, so I understand they're a cause for concern in principle, but they're also only 155bp long and only differ by one base (C/T).
get_org.log.txt slimmed_assembly_graph - Copy.gfa.txt slimmed_assembly_graph - Copy.csv
If this is intended, I suppose the next step would be to manually remove one of the edges from the starting graph and repeat?
Cheers, Seth