Entering edit mode
5.3 years ago
yarivtzur
•
0
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
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.
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"...
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...
That could certainly help I would expect