I would like to know if your bash script supports more than 1 population ID as an outgroup?
While running Treemix directly I have no trouble setting the root to a group of populations as follows
treemix -i spis.18reefs.pop.TM.gz -root FAR_R1,FAR_R2,FAR_R3,FAR_R4 -o spis.18reef.allmarker_rootedFAR > rootedFAR_log
However, when I try to accomplish the same tree rooting strategy using Treemix_bootstrap.sh using the following command:
Treemix_bootstrap.sh spis.18reefs.pop.TM.gz 11 40 500 FAR_R1,FAR_R2,FAR_R3,FAR_R4 100 /home/buitracn/RADseq/tools/phylip-3.697/exe/consense spis.18reefs.pop.allmarkers.FARrooted.m11.100boots.TM
I get the following error:
ERROR in placing root: no clade FAR_R1,FAR_R2,FAR_R3,FAR_R4
Dear BITE developers,
I would like to know if your bash script supports more than 1 population ID as an outgroup?
While running Treemix directly I have no trouble setting the root to a group of populations as follows
treemix -i spis.18reefs.pop.TM.gz -root FAR_R1,FAR_R2,FAR_R3,FAR_R4 -o spis.18reef.allmarker_rootedFAR > rootedFAR_logHowever, when I try to accomplish the same tree rooting strategy using Treemix_bootstrap.sh using the following command:
Treemix_bootstrap.sh spis.18reefs.pop.TM.gz 11 40 500 FAR_R1,FAR_R2,FAR_R3,FAR_R4 100 /home/buitracn/RADseq/tools/phylip-3.697/exe/consense spis.18reefs.pop.allmarkers.FARrooted.m11.100boots.TMI get the following error:
ERROR in placing root: no clade FAR_R1,FAR_R2,FAR_R3,FAR_R4Please advise!