I had a big data set from Miseq to start with mothur and mothur was giving errors that later I realized it is because of RAM and space issue. I tried to divide my sequences file and process them separately until dist.seqs step. then I merged files from to distance files and continue to make shared and taxonomy files. every goes fine except when I get representative otus and tried to run dist.seqs (fasta= clean_repFasta_fileAB.fasta, output=lt) , it gave me an erro: your sequences are not the same length, aborting.
is there any way to get over this error?