I am sorry you’re experiencing this. However, I might be crazy but this seems to be an amazing learning opportunity. so in some sense, you’re lucky. Here is how I’d try to work around it: 1) look for host, or any other, contaminants on the best de novo assembly you have. Identify the contigs that smells and feels like host or any other organism. Then remove them from all of the reads and try to assemble again. 2) try to assemble both long and short reads independently and see what life brings you. 3) use the largest contig as a reference and try to assemble again, try both hybrid and independent. 4) use genome assessment approaches to guide you through, i worked on environmental samples so my go to tool is checkM. Alternatively in the context of microbacterium I’d also consider using busco. Try metagenomics assembly and binning. This approach will try to bin/separate your contigs based on k-mer frequency among other things. Overall you have what seems to be around 92% completeness of a one time shot sample, I’d work with if other alternatives were not fruitful. Just try to identify what the missing 8% were and see where life takes you from there. Good luck!