[root@9adc3a3663e0  00:27:42 /work/my_gwas/01.phylo_tree]# ggtree.r -t fasttree.nwk -f $GROU                                                                                                 P -g Group -n fasttree

WARNING: ignoring environment value of R_HOME

--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/

--> R beginners ? I suggest your  learning  R language: https://study.omicsclass.com/index

Registered S3 methods overwritten by 'treeio':

  method              from

  MRCA.phylo          tidytree

  MRCA.treedata       tidytree

  Nnode.treedata      tidytree

  Ntip.treedata       tidytree

  ancestor.phylo      tidytree

  ancestor.treedata   tidytree

  child.phylo         tidytree

  child.treedata      tidytree

  full_join.phylo     tidytree

  full_join.treedata  tidytree

  groupClade.phylo    tidytree

  groupClade.treedata tidytree

  groupOTU.phylo      tidytree

  groupOTU.treedata   tidytree

  is.rooted.treedata  tidytree

  nodeid.phylo        tidytree

  nodeid.treedata     tidytree

  nodelab.phylo       tidytree

  nodelab.treedata    tidytree

  offspring.phylo     tidytree

  offspring.treedata  tidytree

  parent.phylo        tidytree

  parent.treedata     tidytree

  root.treedata       tidytree

  rootnode.phylo      tidytree

  sibling.phylo       tidytree

ggtree v3.6.2 For help: https://yulab-smu.top/treedata-book/

If you use the ggtree package suite in published research, please cite

the appropriate paper(s):

Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.

ggtree: an R package for visualization and annotation of phylogenetic

trees with their covariates and other associated data. Methods in

Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR

Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package

for phylogenetic tree input and output with richly annotated and

associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.

doi: 10.1093/molbev/msz240

Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan

Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data

object for visualization of a phylogenetic tree and annotation data.

iMeta 2022, 1(4):e56. doi:10.1002/imt2.56

Error in read.table(opt$groupfile, header = T, row.names = 1, check.names = F,  :

  duplicate 'row.names' are not allowed

Execution halted