Hi @Parikrama_Sapkota,
I don't believe that the issue, if you don't have a '#' in your file.
The first link talks about this happening when your feature ids in your rep-seqs aren't the same as the ones in your taxonomy. I think this might be what is going wrong in your case.
Please investigate the feature-ids in both your rep-seqs and taxonomy and verify they are the same!
I hope that helps!
