Sequences are not the same length

I have been trying to pre-process a large datafile using the Costello approach. I started with the raw reads from the sequencer, and trimmed them using my oligos and qual files. Then I used the unique command, followed by alignment with the silva bacterial database. I then screened the data, optimizing to the max and min length and the start and end using a 95% criteria, with maxambig=0 and maxhomop=6. Following this step, the program got stuck in the filter command using the trump symbol (.) and gave me the message that “the sequences are not the same length, please correct”. How do I correct the length of the sequences?

Can you please post the exact command you are entering?

Hello, the command I am entering is:

filter.seqs(fasta=bettyinput2.unique.good.align, trump=.)

About 2400 sequences were filtered before the error message.

I can send you the logfile if necessary.

Yeah, please email the logfile with all of the commands you are entering to