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sriramlab / OrientAGraph

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ERROR: Calling get_child_node_mig on a non-migration node #5

Open huangl07 opened 2 years ago

huangl07 commented 2 years ago

Hi

Today when I was run a new data ,but it turns out like this ?

if I use original treemix， the error is gone？

I wonder know why？

file is in the attach ！

thankyou！ pop.tmix.gz

ekmolloy commented 2 years ago

I will take a look. Can you leave the command that you are using?

huangl07 commented 2 years ago

orientagraph -i pop.tmix.gz -m 5 -o pop.5.2 -k 1000 -bootstrap -global -se -mlno

thank you for reply soon!

thierrygrange commented 1 year ago

This issue is still open for two years. We just stumbled on exactly the same error message: ERROR: Calling get_child_node_mig on a non-migration node and as described herein, the error message was not popping up when using treemix instead of orientgraph. The command we were using was aiming at identifying 5 migrations and it was working well with 4 migrations. In some instances with some datasets we had sporadically the error message and if we relaunched exactly the same command the error was not showing up twice. But here, with 5 migrations, il failed in a recurrent manner. A typical command was orientagraph -i MyData.frq.strat.gz -root MyPreferredBeast -m 5 -k 500 -noss mlno -o MyOutput_5mig_500k_noss. Have you made progress in understanding this issue since 2020? Thanks

ekmolloy commented 1 year ago

This issue is discussed in another post. It's likely that a fifth edge does not change the likelihood score so TreeMix will not add it. If this is the case, you can address this by changing: "-mlno" to "-mlno 1,2,3,4" (so that the MLNO routine is used when adding the first 4 migration edges but not the 5th).

ekmolloy commented 1 year ago

This especially likely to be the problem if you have a small number of populations and a large number of migration edges.