ete3 multicore

[Pieter Coussement]

Hi,

Although I have muliple cores (like most computers), ete3 calculates on a single core.

ete3 build -w mafft_default-none-none-raxml_default_bootstrap -a 1a_fasta_all.fasta -o mafft_default-none-none-raxml_default_bootstrap/ --clearall

How can I fix this.

and second, how can i increase number of bootstrap

[Jaime Huerta Cepas]

Hi Pieter, 

use "--cpu 20" for letting RaxML using 20 threads. 

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[Jaime Huerta Cepas]

sorry, I forgot the second part. To change the number of bootstraps you need to use a custom config: 

$ ete3 build dump raxml_default_bootstrap > myconfig.cfg

- modify the name of the config block, for instance "raxml_default_1000_bootstrap"

- modify number of bootstrap replicates (_bootstrap = 1000) in the options

call ete3 as: 

ete3 build --cpu 20 -c myconfig.cfg -w mafft_default-none-none-raxml_default_1000_bootstrap -a 1a_fasta_all.fasta -o mafft_default-none-none-raxml_default_bootstrap/ --clearall 

[Libusha Kelly]

Hi Jaime! Thank you for this info; when I try to do something similar, I want to modify eggnog41 to use phyml with bootstraps, I get parsing errors. 

I do the following: 

 ete3 build dump eggnog41  > myconfig.cfg

I modify myconfig.cfg such that phyml_default now looks like this: 

[phyml_default]

                                   _desc = Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default models JTT/GTR

                                    _app = phyml

                               _aa_model = JTT

                               _nt_model = GTR

                                  --pinv = e

                                 --alpha = e

                              --nclasses = 4

                                      -o = tlr

                                      -f = m

                             --bootstrap = 100

And I run as follows:

ete3 build -c myconfig.cfg -w eggnog41 -a  v061517.good_prok.200plus.440uniqs.2solos.prots.fasta -o v061517_4_100boot  --clearall

I get the following error: 

ete3.tools.phylobuild_lib.configobj.ConfigObjError: Parsing failed with several errors.

What am I doing wrong? Thank you for providing such an incredible resource. 

Cheers, 

libusha

On Tuesday, November 22, 2016 at 7:06:48 AM UTC-5, Jaime wrote:

sorry, I forgot the second part. To change the number of bootstraps you need to use a custom config: 

$ ete3 build dump raxml_default_bootstrap > myconfig.cfg

- modify the name of the config block, for instance "raxml_default_1000_bootstrap"

- modify number of bootstrap replicates (_bootstrap = 1000) in the options

call ete3 as: 

ete3 build --cpu 20 -c myconfig.cfg -w mafft_default-none-none-raxml_default_1000_bootstrap -a 1a_fasta_all.fasta -o mafft_default-none-none-raxml_default_bootstrap/ --clearall 

On 22 November 2016 at 12:56, Jaime Huerta Cepas <jhc...@gmail.com> wrote:

Hi Pieter, 

use "--cpu 20" for letting RaxML using 20 threads. 

On 22 November 2016 at 12:55, Pieter Coussement <cousseme...@gmail.com> wrote:

Hi,

Although I have muliple cores (like most computers), ete3 calculates on a single core.

ete3 build -w mafft_default-none-none-raxml_default_bootstrap -a 1a_fasta_all.fasta -o mafft_default-none-none-raxml_default_bootstrap/ --clearall

How can I fix this.

and second, how can i increase number of bootstrap

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[Jaime Huerta Cepas]

Hi Libusha, 

sorry for this late response. 

The problem you found is because you have to rename the different config blocks in the dump file. The config parser fails if any of the config blocks exists already in the built in ete3 config. It is also convenient that you change the alias of your custom workflow, so it is not 'eggnog41`. 

 hope it helps, 

-jaime

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