Hi there,
So this is what I type:
mothur > dist.seqs(fasta=16S_juvs_final.fasta, cutoff=0.15)
Output File Name:
16S_juvs_final.dist
It took 1189 to calculate the distances for 20272 sequences.
mothur > cluster(column=16S_juvs_final.dist, name=16S_juvs_final.names)
********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||
unique 3394 15940 1920 679 374 254 152 125 88 74 65 58 56 48 29 23 18 26 23 20 11 26 13 12 9 8 10 7 5 7 6 7 5 1
0.01 4904 9893 1664 682 412 260 168 134 95 82 66 57 60 45 42 29 26 22 28 16 12 17 15 20 14 11 8 12 10 7 7 6 4 1
0.02 5313 5637 1187 576 370 265 171 119 111 77 61 49 46 47 34 39 38 27 24 22 15 22 13 15 14 11 13 8 10 7 5 7 7 14 3 7 6 6 2 5 2 6 3 2 3 3 3 2 6 3 1
0.03 6229 3843 1009 491 315 210 162 122 99 82 54 46 44 29 28 35 27 29 27 17 15 15 18 14 19 10 8 9 13 7 7 5 9 10 8 4 2 4 1 3 1 1 2 1 3 6 1 2 4 2 1
0.04 8885 2914 866 460 276 196 158 119 86 77 62 42 42 34 27 31 23 28 27 17 13 12 18 11 18 5 10 11 11 11 4 5 5 10 7 5 11 10 6 3 5 3 4 0 2 0 2 3 4 4 1
0.05 8954 2394 767 418 248 174 124 131 85 78 51 35 40 33 30 35 23 22 23 15 14 9 15 16 13 4 9 9 7 6 6 6 8 12 4 7 9 8 10 7 7 2 4 2 3 1 1 2 4 2 1
0.06 9169 2029 691 370 237 160 114 110 81 66 51 39 34 32 29 30 29 20 23 18 10 11 10 11 17 7 9 10 12 6 7 4 5 1
changed cutoff to 0.0606444
Output File Names:
16S_juvs_final.an.sabund
16S_juvs_final.an.rabund
16S_juvs_final.an.list
It took 213 seconds to cluster
And I am wondering why it only gives me sequences up to 0.06 cutoff instead of until 0.15?
Thanks
Kim