Hi @Marek_Koutny,
Are you using the same PCR primers for sequencing as you used for DGGE? I agree with you that the general patterns should be consistent between the two approaches, but one reason for a difference could be differences in the PCR primers. Each pair of primers will have biases for different microbial taxa, so you’ll get a different view of the community depending on which primers you’re using. Also, at what taxonomic level are you seeing a lot of differences? At the species level, a lot of differences between the approaches isn’t very surprising, as sequencing 16S doesn’t give very accurate species-level assignments (I think the same is true of DGGE, but I know less about DGGE) - this pre-print has some information on this. At the family level, for example, I’d expect to see a lot more similarity in the profiles derived from DGGE and 16S sequencing.
Regarding your memory error, unfortunately the only way around this will be to run the analysis on a system with more memory. I would recommend trying for 16GB (some discussion of this occurred in this topic).