not enough genes with all species present: master tree has no edge.lengths

[chun-he-316]

Hello! I'm running into an issue when I try to run RERconverge with my data. When I use the function of readTrees , It will prompt me with the following information:

toyTrees=readTrees("TreeFile.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

Then I used the 'estimatePhangornTreeAll' which allowed me to supply the species tree topology as input to get gene trees with the same connectivity (topology) 。

estimatePhangornTreeAll(alndir ="/data/hechun/project/06_Hymeno/11_RERconverge/test/fastas",pattern = "*.fa",treefile="27species.tree.branchLen.nwk",output.file = "estimatePhangornTreeAll.nwk.txt",type = "AA",format = "fasta",k = 4)

But when I run readTrees, I met the same issue.

toyTrees=readTrees("estimatePhangornTreeAll.nwk.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

I have uploaded the treefile created by 'estimatePhangornTreeAll.nwk' . Can you tell me how to solve this problem? I am looking forward to your answer. Thanks. estimatePhangornTreeAll.nwk.txt

[nclark-lab]

Hello, The problem is that there are only 3 trees. These are not enough to provide normalization for all branches since some of the tree have different sets of species. It could be forced to run if you modify the readTrees function to allow fewer trees, but I do not recommend it. The results would not be normalized RERs. If there were more trees, even from genes not related to your process of interest, then it would work. I hope this helps. -Nathan Clark

On Jan 9, 2024, at 4:09 AM, chun-he-316 @.***> wrote:

Hello! I'm running into an issue when I try to run RERconverge with my data. When I use the function of readTrees , It will prompt me with the following information:

toyTrees=readTrees("TreeFile.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

Then I used the 'estimatePhangornTreeAll' which allowed me to supply the species tree topology as input to get gene trees with the same connectivity (topology) 。

estimatePhangornTreeAll(alndir ="/data/hechun/project/06_Hymeno/11_RERconverge/test/fastas",pattern = "*.fa",treefile="27species.tree.branchLen.nwk",output.file = "estimatePhangornTreeAll.nwk.txt",type = "AA",format = "fasta",k = 4)

But when I run readTrees, I met the same issue.

toyTrees=readTrees("estimatePhangornTreeAll.nwk.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

I have uploaded the treefile created by 'estimatePhangornTreeAll.nwk' . Can you tell me how to solve this problem? I am looking forward to your answer. Thanks. estimatePhangornTreeAll.nwk.txthttps://github.com/nclark-lab/RERconverge/files/13871454/estimatePhangornTreeAll.nwk.txt

— Reply to this email directly, view it on GitHubhttps://github.com/nclark-lab/RERconverge/issues/83, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHP5F5AA24EQZ7ZZ7FDPSTTYNUCLTAVCNFSM6AAAAABBSX7UKWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCOJTGI4DIMI. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[nclark-lab]

It is possible to use the minTreesAll option in readTrees for this to work with your dataset. Set minTreesAll = 3 I still don’t recommend this since it would not really normalize the rates well. Best, -Nathan

On Jan 31, 2024, at 8:39 AM, Nathan Clark @.***> wrote:

Hello, The problem is that there are only 3 trees. These are not enough to provide normalization for all branches since some of the tree have different sets of species. It could be forced to run if you modify the readTrees function to allow fewer trees, but I do not recommend it. The results would not be normalized RERs. If there were more trees, even from genes not related to your process of interest, then it would work. I hope this helps. -Nathan Clark

On Jan 9, 2024, at 4:09 AM, chun-he-316 @.***> wrote:

Hello! I'm running into an issue when I try to run RERconverge with my data. When I use the function of readTrees , It will prompt me with the following information:

toyTrees=readTrees("TreeFile.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

Then I used the 'estimatePhangornTreeAll' which allowed me to supply the species tree topology as input to get gene trees with the same connectivity (topology) 。

estimatePhangornTreeAll(alndir ="/data/hechun/project/06_Hymeno/11_RERconverge/test/fastas",pattern = "*.fa",treefile="27species.tree.branchLen.nwk",output.file = "estimatePhangornTreeAll.nwk.txt",type = "AA",format = "fasta",k = 4)

But when I run readTrees, I met the same issue.

toyTrees=readTrees("estimatePhangornTreeAll.nwk.txt", max.read = 200) Read 3 items max is 27 Rotating trees Not enough genes with all species present: master tree has no edge.lengths Naming columns of paths matrix

I have uploaded the treefile created by 'estimatePhangornTreeAll.nwk' . Can you tell me how to solve this problem? I am looking forward to your answer. Thanks. estimatePhangornTreeAll.nwk.txthttps://github.com/nclark-lab/RERconverge/files/13871454/estimatePhangornTreeAll.nwk.txt

— Reply to this email directly, view it on GitHubhttps://github.com/nclark-lab/RERconverge/issues/83, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHP5F5AA24EQZ7ZZ7FDPSTTYNUCLTAVCNFSM6AAAAABBSX7UKWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCOJTGI4DIMI. You are receiving this because you are subscribed to this thread.Message ID: @.***>