Error raised by low-homology references (ValueError: No alignments are stored in the aligner) about clinker

[sminot]

To be clear, I'm only asking this question because clinker has been such an incredibly useful tool! Thank you so much for all your work putting wonderful utility together!

[gamcil]

Glad you find it useful :)

So, clinker internally uses an aligner object which saves all cluster alignments generated during the pipeline - your error should only pop up when attempting to generate the results text summary from that aligner object when no alignments have been generated/saved. In the main clinker workflow, this should be accounted for (i.e. only attempts to generate the summary if there are saved alignments), and the visualisation should work fine regardless.

Even if two clusters don't have any gene links above the threshold, an alignment between them should still be saved, so I think something might be going wrong in the actual alignment stage..

Could you upload some regions that are causing this issue for you? And are you using the most recent version of clinker?

[sminot]

This is very helpful! It appears that this error is coming up for the exact reason you anticipated. This gives me everything I need to fix it on our end. Thanks!