dukecomeback

in case it helps, sometime the problem is caused by the assembly, which should be a line-even fasta.

@katieemelianova One-line fasta refers to those with sequence shown in one-line. So if you less -S it, you will see: \>name1 actgactgactg........ \>name2 gactgactgactg........ I mean by line-even fasta those...