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.txt<https://github.com/nclark-lab/RERconverge/files/13871454/estimatePhangornTreeAll.nwk.txt> — Reply to this email directly, view it on GitHub<#83>, or unsubscribe<https://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.txt<https://github.com/nclark-lab/RERconverge/files/13871454/estimatePhangornTreeAll.nwk.txt> — Reply to this email directly, view it on GitHub<#83>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHP5F5AA24EQZ7ZZ7FDPSTTYNUCLTAVCNFSM6AAAAABBSX7UKWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCOJTGI4DIMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[JhinAir]

Hello, dear @nclark-lab
Hope you are well!

1. I also came across the same issue. However, my input genetree file (from estimatePhangornTreeAll) has enough trees (a total of 15689). It would throw out error as below:

file="All_genes.Phangorn.out"
GeneTrees=readTrees(file, max.read = 400)
..
Not enough genes with all species present: master tree has no edge.lengths
Naming columns of paths matrix

The same error presisted whether I changed the parameters or not: GeneTrees=readTrees(file, max.read = 1000, minTreesAll = 200). I attached the first 1000 genetrees, could you please help check the possible problems?

I also want to discuss another two issues here.
2. The second issue is that when I run with default, it would throw out another error as below:

GeneTrees <- readTrees(file)
..
estimating master tree branch lengths from 15689 genes
Error in allEdgeScaled[, as.character(destinNode.i)] :
no 'dimnames' attribute for array`

3. The third issue occurred when I supply with master tree:

tree2 <- read.tree("241-mammals.filter.nwk")
GeneTrees=readTrees(file, max.read = 500, minTreesAll = 200, masterTree=tree2)
Using readTrees 2
Reading data
Done
Max number of species is 227
Extracting paths
Error in vals[ii] <- treePaths$dist :
NAs are not allowed in subscripted assignments

I guess there is potential issue for the master tree? I also attached it.
Could you please help check these? Thank you very much!

Best regards,
Jing

readTrees.zip

[glhoffmann]

1. It seems your trees themselves don't have enough information for the program to create master tree branch lengths from. However, the master tree itself is still made, just without branch lengths. This doesn't break any further functions, it is just a warning that it is proceeding with a length-less master tree.
2. readTrees doesn't give me any error in the first 10,000 trees. However, there has been an update in RERconverge so I'm using an updated methodology. Try running library(devtools) and install_github("nclark-lab/RERconverge") to reinstall this. If it persists, the issue might be in a tree above index 10000.
3. The master tree you provided does not have the same structure as the other trees - they need to be compatible for RERconverge to work. I've added a warning message for discordant tree topology. If you reinstall RERconverge it should let you know when this is the case.

[JhinAir]

Thank you very much for such quick response! I will try reinstallation.