windows machine; not storing distances to memory

mothur bugs
1

I am running mothur on a windows machine using the executeable. After reading in the distance file and attempting to cluster them into OTUs, I get the following error:

mothur > read.dist(phylip=FD_RL_both_nooutgroup.filter.phylip.dist, group=FD_RL_names.txt)
********************###########
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||

It took 35 secs to read 8 distances (cutoff: 10.005)

mothur > cluster()
Before you use the cluster command, you first need to read in a distance matrix.

Any suggestions? Run on a mac?

Thanks.

2

Can you tell me what version of mothur you are using? Feel free to email me a copy of your distance matrix and we’ll take a look. It shouldn’t matter whether you’re using mac vs pc.

3

When you want to run a cluster after a read.dist you cannot add the group parameter to the read.dist. If you do, mothur thinks you want to use the libshuff command and stores the distances differently. try this…

mothur > read.dist(phylip=FD_RL_both_nooutgroup.filter.phylip.dist)

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

mothur > cluster()

unique 97 774 98 39 25 15 5 8 2 1
0.00 98 602 91 50 28 20 9 7 8 1
0.01 125 360 68 33 28 16 11 8 4 10 7 1 2 1 0 1 0 2 0 1
0.02 199 280 62 30 19 19 6 8 4 1
0.03 235 227 53 30 22 13 10 7 4 10 4 2 2 0 1 0 2 3 0 1
0.04 290 184 48 24 15 12 15 6 5 1
0.05 290 152 49 13 15 10 12 10 6 1
0.06 290 125 42 12 15 10 14 10 5 1
0.07 290 110 39 12 12 5 13 7 4 1
0.08 324 85 30 14 15 3 13 6 5 1
0.09 324 64 26 16 12 5 10 6 4 1
0.10 324 51 27 17 6 6 6 7 2 1
0.11 327 48 23 12 6 7 7 6 1 1
0.12 436 42 22 10 3 6 4 4 2 1
0.13 436 39 18 8 5 6 3 4 3 1
0.14 436 33 16 8 4 4 3 2 2 1
0.15 537 30 15 8 3 5 3 1 3 1
0.16 537 27 13 6 4 1 5 2 3 1
0.17 544 25 8 6 2 1 4 1 1 1
0.18 557 21 10 6 2 1 3 1 1 1
0.19 557 17 11 5 2 1 2 1 2 1
0.20 557 12 9 7 2 1 2 1 2 1
0.21 557 12 9 5 1 0 1 1 1 1
0.22 557 7 7 5 1 1 1 0 0 1
0.23 557 6 6 5 1 1 1 0 0 1
0.24 697 6 4 4 1 1 1 1 0 1
0.25 697 5 4 4 1 1 1 1 0 1
0.26 697 3 4 3 1 1 0 0 0 1
0.27 697 1 2 3 1 0 0 1 0 1
0.28 697 1 2 3 1 0 0 0 0 1
0.29 853 1 2 3 1 0 0 0 0 1
0.30 853 1 2 3 0 0 0 0 0 1
0.31 884 1 2 3 0 0 0 0 0 1
0.32 884 0 2 2 1 0 0 0 0 1
0.33 884 0 2 1 1 0 0 0 0 1
0.35 884 0 2 1 1 0 0 0 0 1
0.36 884 0 1 1 0 0 1 0 0 1
0.37 1111 0 1 1 0 0 1 0 0 1
0.38 1111 0 1 1 0 0 0 0 0 1
0.39 1111 0 0 1 0 0 0 0 0 1
0.41 1111 0 0 1 0 0 0 0 0 1
0.42 1687 0 0 1 0 0 0 0 0 1
0.43 1894 0 0 1 0 0 0 0 0 1
0.44 1947 0 0 1 0 0 0 0 0 1
0.46 1947 0 0 0 0 0 0 0 0 1
0.49 2132 0 0 0 0 0 0 0 0 1

I hope this helps!

4

Thanks!!!