Sequences too short

Hello! I have a problem with my sequences since at the end of the analysis, there are sequences with a length less than 100bp even though I place the analysis parameters to the sequences not to be lower the length than 250bp. When I reviewed the summary sequences they appeared with the correct length. The main change happens from this point:
#dist.seqs(fasta=Army.fasta, processors=30, cutoff=0.20)
#cluster(column=Army.dist, count=Army.count_table, cutoff=0.20, method=average)
#bin.seqs(list=Army.an.unique_list.list, fasta=Army.fasta, label=0.03)
#system(mv Army.an.unique_list.shared Army.an.unique_list.0.03.shared)
#classify.otu(list=current,count=Army.count_table,taxonomy=Army.taxonomy, label=0.03)

I suspect your filter.seqs parameters aren’t quite right to get the right alignment space. I’d look there…