Abra2 creating large (around 100bp) deletions to alignment

[rchapman2000]

Hello,

I have been using abra2 for viral reference based assembly for a while now and have not had any issues. However, recently I have noticed that in a few of my assemblies, there extremely large gaps being added in to the alignment by abra2. It appears that the tool is taking a few bases from the ends of a read and moving to a distant position. It is also odd because these regions do not contain any mismatches from the reference...

Below are screenshots of my alignment before and after running abra2.

Before:

After:

I am currently running abra2 version 2.23 installed via conda.

Let me know what other information I can provide! Thank you!