MiSeq screen.seqs mismaches and minoverlap error

I am trying to clean my MiSeq sequences more thoroughly than in the MiSeq SOP by using the following command after making contigs:

screen.seqs(fasta=filename.trim.contigs.fasta, contigsreport=filename.contigs.report, mismatches=5, minoverlap=25, group=filename.contigs.groups, processors=1)

I have several samples, and in every case I am getting the following error (example numbers):

“[ERROR]: found 101388 sequences in your fasta file, and 101386 sequences in your contigs report file, quitting.”

How can I get the command to work?

Can you post the make.contigs command you ran?

make.contigs(file=filename.files, processors=1)

Could you send your input files to mothur.bugs@gmail.com?