Aligning submodes seems not working

I have split my datasets into several submodes and reconstructed each one, and everything worked well until this stage. After that I aligned the submodes in order to generate a final reconstruction. But it seems like the commend "align_submodels" is not working well. I've checked each submodes folder and there are two json files including "reconstruction.json" and "reconstruction.aligned.json". Interestingly, these two files showed me the same result when visualizing them in the viewer, which means the submodes were not aligned at all. In addition, there is no reconstruction.json in the top layer of the data folder.

Could someone please tell me what's wrong or do I miss something? Thank you in advance for your kind response.

Start by tracing the align_submodels command and compare each submode's reconstruction.json with reconstruction.aligned.json in the viewer. Check how the command handles the data folder's top level, where no reconstruction.json is present. Done should be defined by the expected aligned output and the correct generated reconstruction files.