problem with memory
Pablo V
Hi,
I have been trying to calculate the bootstrap for a phylogeny of ~200 bacterial genomes. However, I cannot manage to obtain any results. So far, I have tried it three times using the following commands:
raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n tree_w_bootstraps -f a -m GTRCAT -# 100 -p 1989 -x 1989 T 8
raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n tree_w_bootstraps2 -f a -m GTRCAT -# 100 -p 1989 -x 1989 T 4
raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n tree_w_50b00tstraps -f a -m GTRCAT -N 10 -p 1989 -x 1989 T 2
I eventually get the following error message:
zsh: killed raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n -f a -m GTRCA
zsh: killed raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n -f a -m GTRCA
zsh: killed raxmlHPC-PTHREADS-SSE3 -s Agro_tax_217_fna_concatenated.aln -n -f a -m GTRCA
When I ran the command the first time, the procedure finished all 100 bootstrapping and was on the Fast ML tree optimisation. The second time I ran the command, the procedure was on the 51st bootstrapping.
I assume that the problem has to do with the memory, but I am not sure how to fix it exactly. Is there an option that could help with memory use? I am running the package in a laptop MacBook Air (processor: 1,6 GHz Dual-Core Intel Core i5, and memory: 8 GB 1600 MHz DDR3) and I am using an external disk for storing the output files.
Thank you for your help!
Cheers,
Pablo
Alexandros Stamatakis
https://cme.h-its.org/exelixis/web/software/raxml/index.html
there is a little web form for calculating the mem reqs of a RAxML analysis.
Alexis
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas
www.exelixis-lab.org