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Error in gene tree processing #3

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fka21 opened this issue Apr 21, 2021 · 10 comments
Closed

Error in gene tree processing #3

fka21 opened this issue Apr 21, 2021 · 10 comments

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@fka21
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fka21 commented Apr 21, 2021

Hello,

First of all let me thank you for setting up this tool, been searching for something like it before. I tried to follow the tutorial provided with my own dataset and provided the same parameters as in the the tutorial, but got the following error message:

Start: species tree processing
Read 1 item
Minimum edge length: 0
Number of short edges ( length < 0.001 ): 6
Transfering branch length from edge 22 to 23 and 60
Transfering branch length from edge 28 to 29 and 50
Transfering branch length from edge 33 to 34 and 37
Transfering branch length from edge 39 to 40 and 43
Transfering branch length from edge 51 to 52 and 59
The tree is not ultrametric. Adjusting the branch length.
Total branch length difference between before- and after-adjustment: 0.0004614733
Nonzero tip age(s) were detected (max=1.4210854715202e-14). Coercing to 0.
End: species tree processing

Start: gene tree processing
Reading NOTUNG tree.
[1] "n2" "n5" "n6"
 Named int [1:3] 12 15 16
 - attr(*, "names")= chr [1:3] "n2" "n5" "n6"
NULL
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: [<- -> [<-.data.frame
In addition: Warning message:
In min(sp_node_table$age[sapply(sp_node_table$spp, function(x) { :
  no non-missing arguments to min; returning Inf

What do you think I am doing wrong?

Cheers
@kfuku52
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kfuku52 commented Apr 21, 2021

Thank you for reporting! Would it be possible to share your input trees?

@fka21
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fka21 commented Apr 21, 2021

Hello, thank you for the quick reply. Not the exact same tree, but another tree which produces the same error. It is the reconciled tree from Notung v2.9.1.5.

(((((Steinernema_carpocapsae_L596_020554:0.0812499,Steinernema_carpocapsae_L596_026598.1:0.162784)n4:0.187569,(Steinernema_feltiae_L889_g3965.t1:0.247091,Steinernema_feltiae_L889_g12653.t1:0.261399)n5:0.174948)n3:1.15416,(((Steinernema_carpocapsae_L596_019371:0.446027,Steinernema_feltiae_L889_g20381.t1:0.766593)n8:0.388058,(Steinernema_carpocapsae_L596_028030.1:0.944139,Steinernema_feltiae_L889_g2036.t1:3.29597)n9:0.48365)n7:0.194342,((((((Steinernema_carpocapsae_L596_020935:0.158974,Steinernema_feltiae_L889_g9453.t1:0.284536)n15:0.0908811,((Steinernema_feltiae_L889_g9452.t1:0.222104,Steinernema_feltiae_L889_g2840.t1:0.0383684)n17:0.180408,Steinernema_carpocapsae_L596_020934:0.696928)n16:0.0774365)n14:0.135463,((((Steinernema_feltiae_L889_g14108.t1:0.0479942,Steinernema_feltiae_L889_g7465.t1:0.316235)n21:0.0884201,Steinernema_feltiae_L889_g4045.t1:6.0E-9)n20:0.186351,Steinernema_feltiae_L889_g3289.t1:0.130419)n19:0.578456,((Steinernema_feltiae_L889_g8486.t1:0.294834,Steinernema_carpocapsae_L596_030428:0.496554)n23:0.235685,((Steinernema_feltiae_L889_g5223.t1:0.0203876,Steinernema_feltiae_L889_g2839.t1:0.0215004)n25:0.305859,Steinernema_carpocapsae_L596_020946:0.205787)n24:0.0339843)n22:0.0593809)n18:0.142929)n13:0.157643,(Steinernema_feltiae_L889_g7917.t2:0.142429,Steinernema_feltiae_L889_g12467.t1:0.105001)n26:0.506928)n12:0.0524064,(((Steinernema_carpocapsae_L596_026600:3.62502,Steinernema_feltiae_L889_g18105.t1:6.0E-9)n29:1.97058,((Steinernema_feltiae_L889_g6086.t1:0.109667,Steinernema_feltiae_L889_g13949.t1:0.339027)n31:0.206936,Steinernema_carpocapsae_L596_027050:0.405061)n30:0.0229929)n28:0.116389,Steinernema_feltiae_L889_g4079.t1:0.417808)n27:0.28686)n11:0.12929,((((Steinernema_feltiae_L889_g11866.t1:0.0860922,Steinernema_carpocapsae_L596_020656:0.722846)n35:0.278392,(Steinernema_feltiae_L889_g2234.t1:0.221814,Steinernema_carpocapsae_L596_019796:0.522306)n36:0.188425)n34:0.124006,((((Steinernema_feltiae_L889_g9666.t1:0.108262,Steinernema_feltiae_L889_g9593.t1:0.0330123)n40:0.0386496,(Steinernema_feltiae_L889_g501.t1:0.204465,Steinernema_feltiae_L889_g500.t1:0.270683)n41:0.0776976)n39:0.377888,(Steinernema_feltiae_L889_g5409.t1:0.0345441,Steinernema_feltiae_L889_g243.t1:0.00302101)n42:0.107822)n38:0.0119802,Steinernema_carpocapsae_L596_020279:0.103429)n37:0.281685)n33:0.036635,((((Steinernema_carpocapsae_L596_014014:0.14299,Steinernema_carpocapsae_L596_014015:0.250342)n46:0.140193,(Steinernema_carpocapsae_L596_019367:0.180108,Steinernema_carpocapsae_L596_019366.1:0.205268)n47:0.0917623)n45:0.0998511,(((Steinernema_feltiae_L889_g8047.t1:5.0E-9,Steinernema_feltiae_L889_g6213.t1:0.0181527)n50:0.227161,Steinernema_carpocapsae_L596_013992:0.0985974)n49:0.272102,((((Steinernema_carpocapsae_L596_020630.3:0.287944,Steinernema_carpocapsae_L596_020629:0.176025)n54:0.0554557,Steinernema_carpocapsae_L596_020628:0.136658)n53:0.0839616,Steinernema_carpocapsae_L596_019368:0.111249)n52:0.132986,(((Steinernema_feltiae_L889_g24605.t1:0.152519,Steinernema_feltiae_L889_g2356.t1:0.0323048)n57:0.00646382,Steinernema_feltiae_L889_g819.t1:0.0166671)n56:0.580582,((Steinernema_feltiae_L889_g5392.t1:0.00283383,Steinernema_feltiae_L889_g5391.t1:0.269966)n59:0.14481,(Steinernema_feltiae_L889_g8709.t1:5.0E-9,Steinernema_feltiae_L889_g10795.t2:0.207903)n60:0.0821074)n58:0.176646)n55:0.0196273)n51:0.0344579)n48:0.0509817)n44:0.0958376,(((Steinernema_feltiae_L889_g17673.t1:0.279278,Steinernema_feltiae_L889_g17672.t1:0.165214)n63:0.295933,((Steinernema_feltiae_L889_g6567.t1:0.17658,Steinernema_feltiae_L889_g22771.t1:0.346269)n65:0.176798,Steinernema_feltiae_L889_g3143.t1:0.162293)n64:0.121925)n62:0.136563,Steinernema_carpocapsae_L596_013994:0.330627)n61:0.132575)n43:0.108698)n32:0.0892593)n10:0.128882)n6:0.0974815)n2:0.208968,Steinernema_carpocapsae_L596_013995:0.326229)n1:0.813658,Ascaris_suum_AgB10_g203_t01:0.813658)n0;

@kfuku52
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kfuku52 commented Apr 21, 2021

Thank you. This looks like a gene tree. I need a species tree too to reproduce the error.

@fka21
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fka21 commented Apr 21, 2021

Oh, my apologies. Below you can find the species tree used.

(Nematostella_vectensis:50,((Branchiostoma_lanceolatum:23.7101,(Danio_rerio:21.6029,(((Bos_taurus:8.70223,Capra_hircus:8.70223)N14:5.68206,(Mus_musculus:13.2604,(Homo_sapiens:7.85935,Macaca_mulatta:7.85935)N17:5.4011)N15:1.12384)N9:5.34555,(Xenopus_tropicalis:18.0441,Gallus_gallus:18.0441)N10:1.68576)N6:1.87307)N4:2.1072)N2:17.8611,(Crassostrea_gigas:35.952,(((Hypsibius_dujardini:26.1183,(Blattella_germanica:16.5116,(((Anopheles_stephensi:10.5211,(((Drosophila_persimilis:4.10651,Drosophila_willistoni:4.10651):0,(Drosophila_ananassae:2.23344,((Drosophila_melanogaster:1.63138,Drosophila_erecta:1.63138):0,(Drosophila_simulans:1.63138,Drosophila_yakuba:1.63138):0)N23:0.602059)N22:1.87307)N20:2.1072,(Drosophila_mojavensis:4.10651,Drosophila_virilis:4.10651)N21:2.1072)N19:4.30736)N18:4.58568,Bombyx_mori:15.1068):0,Tribolium_castaneum:15.1068)N16:1.4048)N11:9.60679)N7:5.61921,(((Steinernema_carpocapsae:6.21372,Steinernema_feltiae:6.21372)N12:4.30736,(Caenorhabditis_elegans:6.21372,Caenorhabditis_angaria:6.21372)N13:4.30736):0,Ascaris_suum:10.5211)N8:21.2165):0,Priapulus_caudatus:31.7376)N5:4.21441)N3:5.61921)N1:8.42882)N0

@kfuku52
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kfuku52 commented Apr 21, 2021

Oops, I needed .parsable file too for the NOTUNG input. Could you also tell me the full radte.r command you tried?

@fka21
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fka21 commented Apr 21, 2021

Here is the parsable file and also the command used. Should've shared these too, sorry.

./radte.r --species_tree=/Users/ferenckagan/Documents/Bioinformatic_analysis/laptop/Bioinformatic_analysis/Phylotranscriptomics/SpeciesTree_rooted_node_labels_binary.txt --gene_tree=/Users/ferenckagan/Documents/Bioinformatic_analysis/laptop/Bioinformatic_analysis/Phylotranscriptomics/Gene_tree_reconciliation/Notung_gene_trees/OG0000999_binary.txt.reconciled --notung_parsable=/Users/ferenckagan/Documents/Bioinformatic_analysis/laptop/Bioinformatic_analysis/Phylotranscriptomics/Gene_tree_reconciliation/Notung_gene_trees/OG0000999_binary.txt.reconciled.parsable.txt --max_age=1000 --chronos_lambda=1 --chronos_model=discrete --pad_short_edge=0.001

81.0   	50     	0      	0      	6      	67     	133    	9      	14     	3      	true   	N8     	N8     	0.00646382,1.97058     	Off    	1      	1      	1.5    	0.0    	3.0    	1.0
Cost   	nD     	nCD    	nT     	nL     	|L(G)| 	|G|    	|S|    	h(G)   	h(S)   	isRoot 	 root(G)       	 root(S)       	minEW,maxEW    	Roots  	Cand   	Feas   	cD     	cCD    	cT     	cL


#D     	Gene Node      	L. Bound       	U. Bound
#D     	n1     	N12    	n316
#D     	n2     	N12    	n316
#D     	n4     	Steinernema_carpocapsae	N12
#D     	n5     	Steinernema_feltiae    	N12
#D     	n6     	N12    	n316
#D     	n7     	N12    	n316
#D     	n10    	N12    	n316
#D     	n11    	N12    	n316
#D     	n12    	N12    	n316
#D     	n13    	N12    	n316
#D     	n14    	N12    	n316
#D     	n17    	Steinernema_feltiae    	N12
#D     	n18    	N12    	n316
#D     	n19    	Steinernema_feltiae    	N12
#D     	n20    	Steinernema_feltiae    	N12
#D     	n21    	Steinernema_feltiae    	N12
#D     	n22    	N12    	n316
#D     	n25    	Steinernema_feltiae    	N12
#D     	n26    	Steinernema_feltiae    	N12
#D     	n27    	N12    	n316
#D     	n28    	N12    	n316
#D     	n31    	Steinernema_feltiae    	N12
#D     	n32    	N12    	n316
#D     	n33    	N12    	n316
#D     	n34    	N12    	n316
#D     	n38    	Steinernema_feltiae    	N12
#D     	n39    	Steinernema_feltiae    	N12
#D     	n40    	Steinernema_feltiae    	N12
#D     	n41    	Steinernema_feltiae    	N12
#D     	n42    	Steinernema_feltiae    	N12
#D     	n43    	N12    	n316
#D     	n44    	N12    	n316
#D     	n45    	Steinernema_carpocapsae	N12
#D     	n46    	Steinernema_carpocapsae	N12
#D     	n47    	Steinernema_carpocapsae	N12
#D     	n48    	N12    	n316
#D     	n50    	Steinernema_feltiae    	N12
#D     	n52    	Steinernema_carpocapsae	N12
#D     	n53    	Steinernema_carpocapsae	N12
#D     	n54    	Steinernema_carpocapsae	N12
#D     	n55    	Steinernema_feltiae    	N12
#D     	n56    	Steinernema_feltiae    	N12
#D     	n57    	Steinernema_feltiae    	N12
#D     	n58    	Steinernema_feltiae    	N12
#D     	n59    	Steinernema_feltiae    	N12
#D     	n60    	Steinernema_feltiae    	N12
#D     	n62    	Steinernema_feltiae    	N12
#D     	n63    	Steinernema_feltiae    	N12
#D     	n64    	Steinernema_feltiae    	N12
#D     	n65    	Steinernema_feltiae    	N12

#LinS  	Species	Losses
#L     	Steinernema_carpocapsae	3
#L     	n316   	0
#L     	N13    	1
#L     	Caenorhabditis_elegans 	0
#L     	Steinernema_feltiae    	2
#L     	Caenorhabditis_angaria 	0
#L     	N12    	0
#L     	Ascaris_suum   	0
#L     	N8     	0

#S     	Species	Dups   	cDs    	Trans_from     	Trans_to       	Losses
#S     	Steinernema_carpocapsae	7      	0      	0      	0      	3
#S     	n316   	0      	0      	0      	0      	0
#S     	N13    	0      	0      	0      	0      	1
#S     	Caenorhabditis_elegans 	0      	0      	0      	0      	0
#S     	Steinernema_feltiae    	24     	0      	0      	0      	2
#S     	Caenorhabditis_angaria 	0      	0      	0      	0      	0
#S     	N12    	19     	0      	0      	0      	0
#S     	Ascaris_suum   	0      	0      	0      	0      	0
#S     	N8     	0      	0      	0      	0      	0

#R     	SpeciesAtRoot
#R     	N8

@kfuku52
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kfuku52 commented Apr 21, 2021

I couldn't reproduce the error... Could you share the all inputs as a zipped file? Copying-and-pasting may cause some troubles. I can fix apparent errors such as the missing semi-colon in the species tree, but there may be something more.

@fka21
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fka21 commented Apr 21, 2021 •
edited
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Here it is:
gene_tree_error.zip

@kfuku52
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kfuku52 commented Apr 21, 2021

I couldn't reproduce the error still but found that the species tree contains non-labeled nodes. I've just updated the radte to return an error for the format violation. Could you retry with the latest radte.r? You should be able to get the correct outputs (below) if the species tree was properly labeled, for example, with the following command.

result.zip

R -q -e "library(ape); t=read.tree('species_tree_noLabel.nwk'); \
t[['node.label']]=paste0('s',1:Nnode(t)); \
write.tree(t, 'species_tree.nwk')"

@fka21
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fka21 commented Apr 21, 2021

The update seemed to have worked. Indeed it pointed out the format violation and after fixing it it works good. 👍 Thank you very much for the help!

@kfuku52 kfuku52 closed this as completed Apr 21, 2021
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