RAXML bootstrapping did not complete the 1,000 replicates as being setup

[Jeremiah Sia]

Dear sir/mdm., 

I would like to inquire why the bootstrapping of the RaxML-NG program i was running did not complete the 1,000 replicates as i have set up. It converged at around 250 replicates. Please advice on how to increase the replicates number before convergence. 

Thank you.

Jeremiah

[Pfeiffer, Wayne]

Hi Jeremiah,

* Please send your _JOBINFO.txt file to cipre...@sdsc.edu.

Thanks,

Wayne

--
You received this message because you are subscribed to the Google Groups "CIPRES Science Gateway Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cipres-science-gatew...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cipres-science-gateway-users/cb569938-41ca-4ab3-bd42-4a645ba69453n%40googlegroups.com.

[Miller, Mark]

Hi Jeremiah,

The run stopped because the run reached convergence.
If you aren’t happy with the result, you can up the convergence stringency.

Clone the job, find the parameter: Specify the bootstrap cutoff value

And make it more stringent.

 

Hope that helps. Let me know if it doesn’t.

 

Mark

[Jeremiah Sia]

Dear Mark and Wayne,

Thank you so much for your replies! It worked after adjusting the bootstrap cutoff value.

Thanks again. 

Regards,

Jeremiah