Default options in clearcut v1.0.9 within mothur 1.48

[eleknagy]

Good evening mothur maintainers,

In my hands, I have noticed two peculiarities when using clearcut v1.09 within mothur 1.48.

• It appears that setting the seed in the clearcut command with, for example, seed=19760620 does not actually set clearcut’s PRNG seed to 19760620 like the standalone clearcut program does.

• Standalone clearcut defaults to Relaxed Neighbor Joining, however mothur seems to default to Neighbor Joining even though the wiki page for clearcut says that “default=F” for the neighbor option.

The MiSeq SOP was followed verbatim, in interactive mode using the full example Stability.MetaG dataset, up until the clearcut step in question.

Specific command and output:
time mothur “#clearcut(phylip=final.phylip.dist, verbose=t, seed=19760620)”

Setting random seed to 19760620.

PRNG SEED: 1737141999
NJ tree built in 4604.359712 secs
NJ tree(s) in final.phylip.tre

real 78m5.783s
user 77m58.793s
sys 0m3.936s

I suppose I was looking for some clarification as to if I am doing something wrong or if these are small bugs.
In the meantime, I will simply update my future workflows to specify neighbor=f.

Best regards and thank you for your time and service maintaining mothur,
Elek

[westcott]

Hi Elek,
Thanks for bringing this issue to our attention. The wiki page and the source inline help differed. In the source ‘neighbor’ defaulted to true, but the wiki indicated it defaulted to false. I have corrected the issue in the wiki and our next release will reflect neighbor=t as the default in both places. The source also used ‘rseed’ instead of ‘seed’ to set the PRNG SEED value. I have changed this to use ‘seed’ in our next release. As a workaround you can run the following with our current version.

mothur > clearcut(phylip=final.phylip.dist, verbose=t, rseed=19760620, neighbor=f)

Kindly,
Sarah