cooccurrence with SIM9

mothur bugs
1

Hi Patrick & Sarah, I don’t know if this is a bug, but when I run cooccurrence with default C score metric and matrixmodel 9 the program stalls. This doesn’t happen if I use default setting (model 2) or model 4, which makes me think my .shared input file is probably OK.

thanks,

Giovanni

2

Hi Giovanni,
Does the program actually crash or does it just seem to hang? Sim9 can take a long time to run on large matrices or if you are doing a lot of iterations.

Thanks,
Kathryn

3

it hangs; it doesn’t crash. I’ll try with fewer iterations and will post another message if problem persists - thanks.

4

Kathryn, reducing the number of iters to 1000 made no difference. The only way I found to run program to completion with SIM9 is to use label=. It’s fine to run like that as I don’t need the scores and p values for all labels. thanks.

Giovanni

5

Could you send your shared and logfile to mothur.bugs@gmail.com so we can try to resolve the bug?

6

Hi Giovanni,
Thanks for sending your files. I took at look at your shared file and mothur is hanging on label 0.63. This is because there is only 1 OTU at that distance. The sim9 matrix model requires at least 2 OTUs to run properly. We are going to add a warning to mothur and in the future mothur will skip labels that contain only one OTU for this model. Thanks for bringing this to our attention.
Kindly,
Sarah