[Molecular-evolution] 16S rRNA based phylogeny and fastDNAmlp
tmargus at ebc.ee
Tue Jun 6 11:03:52 EST 2006
I try to build a 16S rRNA based phylogenetic tree for 160 bacteria and use
for this purpose the parallel version of fastDNAml v1.2.2p (Olsen etal.
1994). Serial version of fastDNAml runs ok (it takes overnight), but if I
try to use parallel version (mpi or pvm) then It can not exceed limit of
130 sequences even during additional 48 h.
The README warns that there is possibility to go to loop, when worker
timeout exceeds 120 sec. then foreman had to decide that worker has to
gone and gives this job to some new worker.
It did not seems to be a case.
I run it with option -d 4 and monitor shows how trees are coming and going
and amount of evaluated trees are exceed 3 000 000.
pvm_dnaml_mon -d 4 -p 16 -n 16srRNA -w /home/tmargus/SSU/ -s
I have increased timeout from 120 sec to 1200 sec and recompiled parallel
version, but without any success.
Had someone face similar problem(s)?
Has someone good idea how to solve it?
Thanks in advance,
Department of Bioinformatics
Institute of Cell and Molecular Biology
University of Tartu
Riia str. 23, Tartu 51010, Estonia
email: tonu.margus at ebc.ee
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