Issues with clearcut

When following the mothur SOP I ran clearcut(phylip=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.phylip.dist)
and the result was
“Killed: 9” and then it exited mothur.

I didn’t run a mock so that is why the file is pick.pick rather than pick.pick.pick.


Most often when we see this issue, it’s caused by the size of the distance matrix. The clearcut command stores the distance matrix in memory. If the size of the matrix is larger than the amount of RAM you have, mothur will crash when it tries to load the file. How big is the phylip file? How much RAM do you have?

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