problems with make.shared

i have followed the analysis tutorial in the Esophageal community analysis but keep running into a problem with trying to execute make.shared in that it only outputs the uniques in the .shared file. I feel that this is a bug as the same commands were run in a previous version with many of the same sequences with out this problem.

Any help would be appreciated

here is what i have run with the output files shown:
mothur > align.seqs(fasta=sample_sequences_all.fas, reference=core_set_aligned.imputed.fasta, flip=T)

Output File Names:

mothur > dist.seqs(fasta=sample_sequences_all.align, output=lt, processors=2)

Output File Name:

mothur > cluster(phylip=sample_sequences_all.phylip.dist, cutoff=0.10)

Output File Names:

mothur > make.shared(, group=sample_sequences_all.groups, label=unique-0.03-0.05-0.10)

Output File Names:

mothur > quit()

Does the .list file contain distances other than unique? What was the previous version used? Could it have been a version of mothur where the default clustering method was furthest? Have you tried running cluster with cutoff=0.25? Have you taken a look at our common questions link? -