Hi @cjain7!

I'm using FastANI to compare a set of approximately 500 MAGs. To do that, I'm executing:

ls -1 -d $PWD/Genomes/*.fna > genome_list.txt
fastANI --rl genome_list.txt --ql genome_list.txt -t 64 -o fastani_output.txt

Across multiple runs I observed that the output varies significantly. For instance, in some cases a comparison of a genome with itself would (a) have a low aligned fraction (~40%), (b) have ~100% of the genome aligned, or (c) wouldn't even show in the output (presumably due to low coverage of the alignment). I've also seen different genomes with high ANI between them (~98%) sometimes appear in the output and sometimes not.

In all my 1 vs. 1 comparisons the output was consistent. The discrepant results appeared only when comparing two lists (in this case, the same list was used as both query and reference).

Here are the output of two independent runs:
dereplicated_mags_ani_raw_1.txt
dereplicated_mags_ani_raw_2.txt

EDIT: I performed a new test using the master branch. The results are still inconsistent and comparisons are missing from all the outputs I'm obtaining.