Lots of outstanding issues though. Could see how far I get with just keeping the original, or see if the Rust conversion could systematically rule out some classes of bugs there... Anyone here actually personally experienced CONCOCT being a pain to use?

Not sure how active this thread is, but I am having issues with CONCOCT consistently crashing with v 5.4.2 due to the inclusion of negative controls in my run. It’s important for me to process and assemble any MAGs that may be in these negative controls , and the other binners seem to do just fine with it. Any insights on this would be appreciated. I may just add the --skip_concoct flag since I have multiple binners already feeding into DASTool

Hah, and so you found my thread... Unfortunately I gave up on rewriting CONCOCT because the C++ core was hard to optimize (already kinda well-written, the "it's all python hot loops" turned out to be false)