Mobile element calling code contains an assertion that both sets of vertices come from the same mobile element. We have found cases where this fails:
# in genome_finish/graph_contig_placement.py
>translocation_seq_verts
[ME_insertion_sequence:IS150_RC_121, ME_insertion_sequence:IS186_RC_253]
This could be because the mobile elements look similar at the alignment region.
There are two ways to fix this:
1) ignore these mobile elements (not ideal)
2) combine them with (IS150/IS186)
I think this is just a really confusing highly paralogous region. I blasted the contig and just got more confused. However, there is definitely an IS element involved here:
Mobile element calling code contains an assertion that both sets of vertices come from the same mobile element. We have found cases where this fails:
This could be because the mobile elements look similar at the alignment region.
There are two ways to fix this: 1) ignore these mobile elements (not ideal) 2) combine them with (IS150/IS186)
I think this is just a really confusing highly paralogous region. I blasted the contig and just got more confused. However, there is definitely an IS element involved here: