Error in gene tree processing

[fka21]

Error in gene tree processing

[fka21]

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]

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

[fka21]

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]

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

[fka21]

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]

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

[fka21]

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]

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]

Here it is:
gene_tree_error.zip

[kfuku52]

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')"