What does NA mean in the result of fastANI matrix output?

Question

[Antonio]

Hello.

It may be a silly question, but the result within the matrix values represented by NA can be any value?

Or is there a cutoff limit for the values?

I'm just starting to use the tool, I'm learning how to use it.

If this cut limit occurs, can I remove this restriction on the command line? I need all the values, even if they are lower than expected.

Thanks.

Herbaspirillum sp K1R23-30.fasta 78.250549 NA NA 78.578194 78.588776 78.285095 78.805077 78.449890 78.417480 78.283737 78.185516 78.336975 78.355698 78.523407 78.693100 78.352158 78.382851 78.300049 NA NA NA NA NA NA 78.072609 77.977020 78.465851 78.434601 78.444366 78.532547 78.185631

fastANI --threads 4 --ql querylist.txt --rl reflist.txt --matrix -o fastani.out

[Wayne]

The README documentation does link to an alternative way to calculate ANI as BLAST-based ANI solver perhaps that would allow you use your genomes. It looks like there you can adjust the minimum identity. And it looks like that includes making alignments based on it having a section for 'Alignment options'.
Whereas FastANI is 'fast alignment-free computation'.

---

From the FastANI README documentation:

Running the following will give all the command line options for FastANI:

./fastANI -h

There's also pertinent information in the FastANI README documentation explaining why you are seeing reports of NA:

"NOTE: No ANI output is reported for a genome pair if ANI value is much below 80%. Such case should be computed at amino acid level."

And the accompanying paper:

FastANI is targeted to estimate ANI in the 80–100% identity range. Therefore, it calls Mashmap mapping routine with an identity cutoff I0 = 80%, which enables it to compute mappings with alignment identity close to 80% or higher."

I think you are out of luck. For it to be efficient the developers have set this as a target cut-off.
You can see the setting hard-coded into the code here. If yours isn't far off you may be able to push it by changing that and recompiling. A huge drawback is that your runs of FastANI then wouldn't be comparable to others reporting values from it.

[Antonio]

Thank you very much Wayne.

Answered my doubts.

Best Regards.