how to use PUG?

[ShuaiNIEgithub]

The PUG looks like a great tool for studing WGD. However, I don't get any results when I use demo data. So, could you give me some advises?

This is my code:
cd PUG/PUG_Test_Data
rm *txt *Species_Tree*
echo "Dichanthelium" > outgroupspecies
perl ../PUG.pl --trees PUG_demo_trees --species PUG_demo_tree.tre --outgroups outgroupspecies

[mrmckain]

Do you have any other information? Other outputs or errors?

[ShuaiNIEgithub]

Hi,McKain.
Thanks for your reply. I can certainly show you more information:

#1. Installion code:

cd ~/bin
git clone https://github.com/mrmckain/PUG.git

#2. Input:
PUG_demo_trees #demo file
PUG_demo_tree.tre #demo file
outgroupspecies #I use "Dichanthelium" as outgroup species here.

#3. Run code:

cd ~/bin/PUG/PUG_Test_Data
rm *txt *Species_Tree*
echo "Dichanthelium" > outgroupspecies
perl ../PUG.pl --trees PUG_demo_trees --species PUG_demo_tree.tre --outgroups outgroupspecies

#4. Output:
After 3 minutes of running the program, no error information appears, and then a total of 9 result files are obtained.

• Content is empty (four files)：

PUG_Gene_Tree_Results.txt, PUG_Gene_Trees_Pairs_Bad_Results.txt, PUG_Paralog_Pairs_Per_Tree.txt, PUG_SUMMARIZED_5080.txt

• cat PUG_Paralog_Pairs_Nodes_Bootstraps.txt #Only one row is the column name

Orthogroup Node Bootstrap Paralog1 Paralog2

• tail PUG_Labeled_Species_Tree.eps #sample as demo file "PUG_Demo_Labeled_Species_Tree.eps"

270 10 moveto
250 10 lineto
251.2 16 moveto
(N15) show
250 10 moveto
250 20 lineto
30 494.7802734375 moveto
10 494.7802734375 lineto
stroke
showpage

• cat PUG_Labeled_Species_Tree.tre #sample as demo file "PUG_Demo_Labeled_Species_Tree.tre"`

(Dichanthelium, ((Setaria,Panicum)N1, ((Arundinella-hookeri, Arundinella-hirta)N2, (Thelepogon, ((Arthraxon,Chrysopogon)N3, (((Urelytrum,Vossia)N4, ((Zmays, Zea-perennis)N5,(Tripsacum-dactyloides, (Tripsacum-cundinamarce, (Tripsacum-australe, Tripsacum-peruvianum)N6)N7)N8)N9)N10, (Chionachne, ((Hemarthria,Coelorachis)N11, (Ischaemum, (((Saccharum, Miscanthus)N12, Sorghum)N13, ((Bothriochloa, Dichanthium)N14, (Andropogon, Schizachyrium)N15)N16)N17)N18)N19)N20)N21)N22)N23)N24)N25)N26;

• head -n2 PUG_Summary_Results.txt #all nodes are "0"

Event   Species_Tree_Node       100     99      98      97      96      95      94      93      92      91      90      89      	88	87       86      85      84      83      82      81      80      79      78      77      76      75      74      73      72     	71	70       69      68      67      66      65      64      63      62      61      60      59      58      57      56      55    	 	54	53       52      51      50      49      48      47      46      45      44      43      42      41      40      39      38      	37	36       35      34      33      32      31      30      29      28      27      26      25      24      23      22      21      	20	19       18      17      16      15      14      13      12      11      10      9       8       7       6       5       4       	3		2		 1       0
unknown N1      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 	0	0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 	0	0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0 	0	0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0	 0	0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0	 0	0       0       0       0       0       0       0       0       0       0       0       0       0

[mrmckain]

I did a fresh download and ran using your commands. The use of 'echo "Dichanthelium" > outgroupspecies' to set the outgroups does not work. This is read as "outgroupspecies" not the file. You should just use --outgroups "Dichanthelium". Since you are not setting a BSV, the outputs will be slightly different the the ones packaged with the script.

[Dawei-Xia]

How to view WGD result from output files?
The PUG looks like a great tool for studing WGD. However, i get 9 results files when I use demo data and a "New_File_Name.pdf" after run "Rscript PUG_Figure_Maker.R PUG_Labeled_Species_Tree.tre PUG_SUMMARIZED_5080.txt New_File_Name.pdf", i don’t know how to deduce WGD node ？So, could you give me some advises？ Looking forward to your reply