Can't read input files: "list index out of range"

[kriskaykj]

Hello,

I am trying to compare two phylogenies on both the GUI and the CLI, but in both I get an error: "Error: cannot read host file path/to/file/host.nwk: list index out of range".

My host file looks like this: ((MT445.1_rc_rotated,((MN164.1_rc_rotated,MN164.1_rc_rotated),MN164.1_rc_rotated)),(((((MN164.1_rc_rotated,((Coci-NEP-7-notrim.,(((NeHi3-notrim.,NeHi4-notrim.),NeVoMP5-trim2.),(NeVoMP2-trim2.,NeVoMP3-trim2.))),ptg000021l_rc_rotated)),NeVoMP4-trim2.),(Coci-NEVO-2-trim2.,(NeVo4-trim2.,NeVo6-trim2.))),(NeVoKM2.,NeVoKM7-trim2.)),(((((NeHiPe6.,NeHiPe9.),NeHiPe7.),NeHiPe8.),(NeVoKD2-trim2.,(((NeVoKD3-trim2.,NeVoKD6-trim2.),(NeVoKD5.,NeVoKD7.)),NeVoKD4-trim2.))),(NeVoKD1_total_trim2.,NeVoKM8-trim2.))),KT874.1_rc_rotated);

I'm not sure what it is having an issue with. Thank you in advance!

[Jessica555lab]

"Error: cannot read host file path/to/file/host.nwk: list index out of range". My host file looks like this: (C3e-06,C27-C21-C3,((((((((C1-C1c-C1b-C72k-C3,C1)e-05,C1-C1b-C1u-C3-C1bo),C1/C3u-C3-C1c-C1b),(C15/C1-2506_C,2506)),(((((C15-1541,C15e-08),1826),C3u-C3-1425),C3u/C3-C21ab-C115-1367_C),C3u/C3/C21a-C21)),C21a-C21-C3-C21k),((1531,C66),(((C17f,13923),C26-1449-C21ac-1451-1450-C21-1452),C17f/C1-C1c)))e-05,(C50c/C3-C50a-C50f-1391_C-C3b-C3ad,C3/C50c-C50a-C3b-C3.10))e-05);

[Jessica555lab]

"Error: cannot read host file path/to/file/host.nwk: list index out of range". (D,(C3,H,((((((((C1-C1c-C1b-C72k-C3,C1),C1-C1b-C1u-C3-C1bo),C1/C3u-C3-C1c-C1b),(C15/C1-2506_C,2506)),(((((C15-1541,C15),1826),C3u-C3-1425),C3u/C3-C21ab-C115-1367_C),C3u/C3/C21a-C21)),C21a-C21-C3-C21k),((1531,C66),(((C17f,13923),C26-1449-C21ac-1451-1450-C21-1452),C17f/C1-C1c))),(C50c/C3-C50a-C50f-1391_C-C3b-C3ad,C3/C50c-C50a-C3b-C3.10))));

[Jessica555lab]

i don;t know how to do

[emilyvansyoc]

It looks like the developer has not been able to fix this bug as I am having the same issue...

[fantine-bodin]

Hello, I also had this error and I fixed it by deleting node labels in my tree file. I have a R code where I prepare the files before empress and I added this line to the code : host_tree$node.label <- NULL I hope this will solve your issue !

[Ofsm]

Ey, I'm having the same problem!, I founded that you probably need to collapse single tips in the tree (using ape). You could also add nodes labels to your trees (h=host, p=parasites), here is the way I solved it:

TreeH<-read.tree("Host_eMPR.nwk") # host tree TreeH<-makeNodeLabel(TreeH, method = "number", prefix = "h") #add nodes labels, here I used numbers and prefix "h", so h1 is node 1 and so on, and so on TreeH<-collapse.singles(TreeH) # collapse single tips ape::write.tree(TreeH, file='~/Desktop/eMPRess/host_nodes.txt') # exporting tree from R to my working directory (format is nwk, so you can change the extension later to .nwk or .tree)

Hope this help

[fmassive]

Ey, I encountered the same issue. After reviewing the input files and comparing them with the example data provided, I found that the example data were all rooted trees, whereas my input files were unrooted trees. Once I converted my unrooted trees to rooted trees in R, the problem was resolved. rooted_tree <- root(unrooted_tree, outgroup = "Outgroup_Species", resolve.root = TRUE)

[ssantichaivekin]

I'm not a .nwk expert myself and use a library to help read this format. If @fantine-bodin and @fmassive happen to have a "before and after" examples, I'm happy to implement the same auto-fix in the code.

[ssantichaivekin]

@kriskaykj Looks like some of the nodes of your tree has 3 children, which we do not support. I will admit that the current error message is very bad though. I will look into fixing it. Same with @Jessica555lab