@ahaponski_twitter Is it denovo or reference based? If you look in your output/*_stats.txt file right at the top it indicates the results of different filters applied, maybe there's a clue there? What was the average number of loci recovered per sample? 0.6.17 is quite old, the 0.7 version update was significant, and there have been a lot of minor bug fixes since then, so it's really hard to say what's causing the difference without really digging into the data. In the absence of other evidence I would suggest sticking with results from the most recent version.