how to read cluster() output?

Commands in mothur
1

I have an alignment of 5670 sequences, but when I cluster it, I get 8159 unique sequences in the largest OTU. How is it possible to have more sequences in an OTU than there are sequences in the alignment?

mothur > summary.seqs(fasta=auw.unique.good.good.filter.fasta)


Start End NBases Ambigs Polymer Minimum: 1 213 170 0 3 2.5%-tile: 1 213 196 0 3 25%-tile: 1 213 207 0 4 Median: 1 213 211 0 5 75%-tile: 3 213 211 0 5 97.5%-tile: 3 213 213 1 6 Maximum: 3 213 213 1 8 # of Seqs: 5670

mothur > read.dist(column=auw.msa.dist,name=auw.names)

********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

It took 7 secs to read

mothur > cluster(cutoff=0.03)

unique 8159 43325 6600 2483 1379 849 557 387 292 206 155 125 112 89 51 33 41 35 35 40 22 27 24 14 23 9 13 14 16 11 11 9 6 8 9 10 5 11 9 3 4 1 5 6 7 6 3 1
0.00 8159 42337 6564 2498 1403 877 588 412 298 207 158 132 109 92 54 39 39 35 34 43 22 26 26 14 21 10 13 14 17 9 12 10 5 7 9 10 9 3 3 1 6 5 9 6 3 7 6 1
0.01 8159 41104 6250 2341 1330 858 559 403 313 217 173 135 110 93 55 37 44 34 34 41 26 28 30 18 22 9 15 14 17 11 12 9 7 8 9 10 9 4 4 1 5 6 7 6 3 7 7 1
0.02 8159 40864 6183 2300 1303 823 537 384 284 207 155 131 107 86 53 35 42 37 36 44 23 29 31 18 25 13 15 14 16 10 10 9 5 6 10 10 6 12 9 3 5 2 5 6 7 6 5 1
0.03 8159 40769 6136 2294 1297 812 534 379 283 205 149 127 107 85 53 36 39 34 33 46 22 29 29 17 23 10 14 16 18 9 12 9 5 8 10 11 10 3 4 1 5 5 9 7 3 9 6 1
It took 27 seconds to cluster

2

forgot to mention, I renamed auw.unique.good.good.filter.fasta to auw.msa.fasta (for brevity).

3

I think the names file is the problem. It looks like you’ve run screen.seqs twice and I wonder if you included the names file in those commands or if you used the correct names file in read.dist.