Comments (10)
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!
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Thank you for reporting! Would it be possible to share your input trees?
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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;
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Thank you. This looks like a gene tree. I need a species tree too to reproduce the error.
from radte.
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
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Oops, I needed .parsable file too for the NOTUNG input. Could you also tell me the full radte.r
command you tried?
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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
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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.
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Here it is:
gene_tree_error.zip
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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.
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')"
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