Question: Fasttree crashing out of memory when building large species tree
gravatar for yarivtzur
9 months ago by
yarivtzur0 wrote:

Hi, I am trying to use the latest Fasttree to construct a phylogenetic tree out of a nucleotide alignment of concatenated CDS of 2500 strains of Pseudomonas Aoruginosa (the alignment file is 5GB). I am running Fasttree on a strong server with 150Gb of ram, however Fasttree is unable to complete its run and at some point runs out of memory and crashes. Is there someway to make Fasttree only work with the memory it has? If not, can anyone recommend a tree building tool that is up to the task? Thanks

software error • 342 views
ADD COMMENTlink written 9 months ago by yarivtzur0

Are you certain it’s a memory issue? I would have expected fasttree to be OK with an alignment even that large with that much ram.

ADD REPLYlink written 9 months ago by Joe14k

At first the process was killed with a message printed "killed", and I could see it was killed by the OS in /var/log/messages for out of memory. Then I tried to limit its memory to 140 gb with ulimit -s 140000000 -v 140000000, and then the process died and prints "out of memory"...

ADD REPLYlink written 9 months ago by yarivtzur0

It seems the issue is only happening with the FastTreeMP and FastTreeDbl versions that I downloaded, the regular FastTree executable successfully ran without running out of memory. Not sure why the other 2 versions failed, maybe I needed to compile them on my machine...

ADD REPLYlink written 9 months ago by yarivtzur0

That could certainly help I would expect

ADD REPLYlink written 9 months ago by Joe14k
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