bqminh
commented
4 years ago Can you pls provide the date file? Is the date in the right format YYYY-MM-DD?
Open Juanphg opened 4 years ago
bqminh
commented
4 years ago Can you pls provide the date file? Is the date in the right format YYYY-MM-DD?
Juanphg
commented
4 years ago Hello Mihn, No, are fossil dates, with maximum and minimum (max:min) The file is attached. Thanks, Juan P
El jue., 4 de jun. de 2020 a la(s) 12:08, Bui Quang Minh ( notifications@github.com) escribió:
Can you pls provide the date file? Is the date in the right format YYYY-MM-DD?
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Boa_constrictor,Eryx_colubrinus -93.9:-58 Afronatrix_anoscopus,Aplopeltura_boa,Atractaspis_micropholis,Azemiops_feae,Bitis_arietans,Bothriechis_schlegelii,Buhoma_depressiceps,Buhoma_procterae,Bungarus_ceylonicus,Calamaria_pavimentata,Calliophis_melanurus,Cerberus_rynchops,Coluber_constrictor,Compsophis_infralineatus,Crotalus_adamanteus,Cubophis_cantherigerus,Daboia_russelii,Dendroaspis_angusticeps,Diadophis_punctatus,Drymarchon_corais,Erpeton_tentaculatum,Gonionotophis_brussauxi,Grayia_ornata,Helicops_infrataeniatus,Hormonotus_modestus,Hydrophis_curtus,Imantodes_cenchoa,Laticauda_colubrina,Laticauda_laticaudata,Leioheterodon_madagascariensis,Madagascarophis_colubrinus,Malpolon_monspessulanus,Micruroides_euryxanthus,filiformis_ICN11380,sp_INSSRMiclem5,Naja_naja,Natrix_natrix,Nerodia_sipedon,Ninia_atrata,Ophiophagus_hannah,Oxyuranus_microlepidotus,Pareas_hamptoni,Plagiopholis_styani,Psammophis_mossambicus,Pseudechis_australis,Pseudoxenodon_karlschmidti,Rhinocheilus_lecontei,Salvadora_hexalepis,Scaphiodontophis_annulatus,Sibynophis_collaris,Simoselaps_anomalus,Sinomicrurus_macclellandi,Thamnophis_sirtalis,Thermophis_baileyi,Thermophis_zhaoermii,Toxicocalamus_preussi,Trimeresurus_stejnegeri,Vipera_eriwanensis,Xenocalamus_transvaalensis,altirostris_MCP5035,altirostris_IB55595,baliocoryphus_MZUSP10808,brasiliensis_CEPB2301,brasiliensis_IB55385,circinalis_UWIZM2016_22,corallinus_CEPB051,diastema_RH52446_M50,dissoleucus_UTAM673,diutius_CAS231787,lemnicatus_MPEG19054,diutius_UWIZM2012_4,diutius_UWIZM2016_24,elegans_M22,frontalis_CEPB1587,frontalis_CEPB2365,fulvius_GU045453,ortoni_QCAZ2584,ortoni_LSUMZH1529,ibiboboca_YPX161,carvalhoi_CEPB2687,helleri_CEPB2289,lemniscatus_CAS257629,filiformis_Piranha,sp_ICN13077,sp_ICN13076,sp_INSVSRMicfil1,sp_INSVSRMiclem2,sp_INSVSRMicfil2,cf_ibiboca_IVB1757,cf_ibiboca_CEPB2312,carvalhoi_IB55598,diutius_ROM22835,mipartitus_CH5377,mipartitus_MHUAR14488,narduccii_WED54125,nigrocinctus_M13,obscurus_KU222205,pyrrhocryptus_MZUSP10809,pyrrhocryptus_LSUMZH6130,obscurus_CEPB1807,surinamensis_LJV7110,surinamensis_Vidal_KU214908,tener_FTB2189_M449 -93.9:-58 Afronatrix_anoscopus,Calamaria_pavimentata,Coluber_constrictor,Cubophis_cantherigerus,Diadophis_punctatus,Drymarchon_corais,Grayia_ornata,Helicops_infrataeniatus,Imantodes_cenchoa,Natrix_natrix,Nerodia_sipedon,Ninia_atrata,Plagiopholis_styani,Pseudoxenodon_karlschmidti,Rhinocheilus_lecontei,Salvadora_hexalepis,Scaphiodontophis_annulatus,Sibynophis_collaris,Thamnophis_sirtalis,Thermophis_baileyi,Thermophis_zhaoermii -54:-35.2 Bothriechis_schlegelii,Crotalus_adamanteus,Trimeresurus_stejnegeri -54:-11.2 Cubophis_cantherigerus,Diadophis_punctatus,Helicops_infrataeniatus,Imantodes_cenchoa,Ninia_atrata -54:-12.5 Bungarus_ceylonicus,Calliophis_melanurus,Dendroaspis_angusticeps,Hydrophis_curtus,Laticauda_colubrina,Laticauda_laticaudata,Micruroides_euryxanthus,Naja_naja,Ophiophagus_hannah,Oxyuranus_microlepidotus,Pseudechis_australis,Simoselaps_anomalus,Sinomicrurus_macclellandi,Toxicocalamus_preussi,altirostris_IB55595,altirostris_MCP5035,baliocoryphus_MZUSP10808,brasiliensis_CEPB2301,brasiliensis_IB55385,carvalhoi_CEPB2687,carvalhoi_IB55598,cf_ibiboca_CEPB2312,cf_ibiboca_IVB1757,circinalis_UWIZM2016_22,corallinus_CEPB051,diastema_RH52446_M50,dissoleucus_UTAM673,diutius_CAS231787,diutius_ROM22835,diutius_UWIZM2012_4,diutius_UWIZM2016_24,elegans_M22,filiformis_ICN11380,filiformis_Piranha,frontalis_CEPB1587,frontalis_CEPB2365,fulvius_GU045453,helleri_CEPB2289,ibiboboca_YPX161,lemnicatus_MPEG19054,lemniscatus_CAS257629,mipartitus_CH5377,mipartitus_MHUAR14488,narduccii_WED54125,nigrocinctus_M13,obscurus_CEPB1807,obscurus_KU222205,ortoni_LSUMZH1529,ortoni_QCAZ2584,pyrrhocryptus_LSUMZH6130,pyrrhocryptus_MZUSP10809,sp_ICN13076,sp_ICN13077,sp_INSSRMiclem5,sp_INSVSRMicfil1,sp_INSVSRMicfil2,sp_INSVSRMiclem2,surinamensis_LJV7110,surinamensis_Vidal_KU214908,tener_FTB2189_M449 -54:-24.9 Afronatrix_anoscopus,Natrix_natrix,Nerodia_sipedon,Thamnophis_sirtalis -54:-13.8 Oxyuranus_microlepidotus,Hydrophis_curtus,Pseudechis_australis,Simoselaps_anomalus,Toxicocalamus_preussi -54:-10 Vipera_eriwanensis,Bitis_arietans,Azemiops_feae,Bothriechis_schlegelii,Crotalus_adamanteus,Daboia_russelii,Trimeresurus_stejnegeri -93:-22.1
bqminh
commented
4 years ago Can you pls try v2.0.6, from the release tab. It fixes a few bugs in LSD2
bqminh
commented
4 years ago Juanphg
commented
4 years ago Hello Mihn, I already run it again in the new version. Now it reads the correct ammount of dates in the DATE_FILE, but afterwards is showing me the same error. Do you think is a problem on how I prepared the files for dating or on my computer? Because, otherwise, I'm obtaining the ML tree without problems. This is the error: --- Start phylogenetic dating --- Reading date file dating_iq_2.txt ... 9 dates extracted Building time tree by least-square dating (LSD) with command: lsd -i best_scheme_realligned_PF_20200602.txt.timetree.subst -s 3652 -o best_scheme_realligned_PF_20200602.txt.timetree -g best_scheme_realligned_PF_20200602.txt.timetree.outgroup -d best_scheme_realligned_PF_20200602.txt.timetree.date -z 0 Reroot the tree 1 using given outgroups ...
TREE 1 *PROCESSING: Reading the tree ... Collapse 4 (over 107) internal branches having branch length <= 0.000137 (settable via option -l) Parameter to adjust variances was set to 0.0415 (settable via option -b) ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: best_scheme_realligned_PF_20200602.txt.log ERROR: Alignment files (if possible)
Thanks again for your help.
Cheers, Juan P.
El vie., 5 de jun. de 2020 a la(s) 01:47, Bui Quang Minh ( notifications@github.com) escribió:
https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6
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bqminh
commented
4 years ago @tothuhien can you pls help? It seems some problem within LSD2...
@Juanphg can you pls rerun with --date-debug option, and then send Hien the files, which are listed in lsd command, necessary to debug LSD2.
Thanks
Juanphg
commented
4 years ago Hello @bqminh and @tothuhien Juanphg.zip Attached you will find the files I used to run the analysis and the log file. Please let me know if you need something else.
Thanks again for your help,
Cheers,
Juan P
tothuhien
commented
4 years ago Hi Juan, could you give me the tree generated by iq-tree as well? @bqminh : I've updated lsd2 some days ago to fix a bug about given fossil dates. Not sure that concerns this problem because I need the tree to debug, but when you have time could you update it to iq-tree?
Hien
Juanphg
commented
4 years ago Hello, Here goes the tree.
Cheers
El jue., 11 de jun. de 2020 a la(s) 20:50, Thu-Hien To ( notifications@github.com) escribió:
Hi Juan, could you give me the tree generated by iq-tree as well? @bqminh https://github.com/bqminh : I've updated lsd2 some days ago to fix a bug about given fossil dates. Not sure that concerns this problem because I need the tree to debug, but when you have time could you update it to iq-tree?
Hie
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tothuhien
commented
4 years ago Hi, could you attache the file again? I don't see it.
Juanphg
commented
4 years ago Here it goes again. I forgot that .tre files are not accepted here. IQ.txt
tothuhien
commented
4 years ago Thanks. I run your data with the new updated lsd2 and there's no problem. So I think that concerns the last bug that I've fixed. Could you include that in iq-tree @bqminh . There's not any change in parameter setting structure, just some small changes in 1 file, you'll see.
For you data, I tested the dating process with this with the command
./lsd2 -i Juanphg/IQ.txt -d Juanphg/date.txt -s 3652 -g outgroup.txt -z 0 -f 100
and results:
Reroot the tree 1 using given outgroups ...
TREE 1 PROCESSING: Reading the tree ... Collapse 4 (over 106) internal branches having branch length <= 0.000136911 (settable via option -l) Parameter to adjust variances was set to 0.0436524 (settable via option -b) Minimum branch length of time scaled tree (settable via option -u and -U): 0.0280775, rounded to 0.0273973 (10 days/365) using factor 365 (settable via option -R) Estimating the root position on the branch defined by given outgroups ... Computing confidence intervals using sequence length 3652 and a lognormal relaxed clock with mean 1, standard deviation 0.2 (settable via option -q) RESULTS:
and the dated tree
bqminh
commented
4 years ago I have quickly updated lsd v1.8.1 Can you pls re-download iqtree here: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6
Juanphg
commented
4 years ago Hello @tothuhien and @bqminh Thanks for the help. Those results match almost exactly with the ones I obtained with beast. Nevertheless, when I tried to rerun the analyses in IQ, several times, with the same data and with some modifications, I had error and the resulting trees had really strange values. The attached logfile was obtained with the exact same data I sent before. Additionally, I noted that this time in the resulting dated trees they didn't read the outgroups in the input tree. The commands I used are: iqtree-2.0.6-Windows\bin\iqtree2.exe -s allignment.phy -p partitions.txt -te iq.txt --date Dating_file.txt --date-ci 100 -T 4
Attached is also the resulting nexus tree. partitions.txt.timetree.nex.txt
Thanks a lot, Cheers
tothuhien
commented
4 years ago Hi, did you forget to set tips date = 0 (--date-tip 0) ?
Hien
Juanphg
commented
4 years ago Hello, sorry for my late answer. Actually, I did forget. Nevertheless, despite the analysis runs, I'm still getting some errors that I'm not sure how it affects the results. Also, the values are higher than in the tree @tothuhien sent and despite being annotated in the tree, figtree o R packages don't read the CI values. These were the commands I used: iqtree2.exe -s allignment.phy -p partitions.txt -te iq.txt --date Dating_file.txt --date-tip 0 --date-ci 100 Here are the results (also the tree is attached): TREE 1 PROCESSING: Reading the tree ... Collapse 4 (over 105) internal branches having branch length <= 0.000137 (settable via option -l) Parameter to adjust variances was set to 0.0399 (settable via option -b) Can not estimate minimum branch lengths for time scaled tree: the temporal constraints provided are not enough, or conflict. Minimum branch length is then set to 0 (settable via option -u and -U). Estimating the root position on all branches using fast method ... Computing confidence intervals using sequence length 3652 and a lognormal relaxed clock with mean 1, standard deviation 0.2 (settable via option -q) WARNINGS:
TOTAL ELAPSED TIME: 0.327 seconds LSD results written to: LSD report: partitions.txt.timetree.lsd Time tree in nexus format: partitions.txt.timetree.nex Time tree in newick format: partitions.txt.timetree.nwk partitions.txt.timetree.txt
Thanks again,
Cheers, JP
tothuhien
commented
4 years ago Hi, is it exactly the same data that you sent me last time? If you did some modifications, could you send me again the input tree and the input date file?
Hien
tothuhien
commented
4 years ago and could you tell me which figtree version and os you use to load the nexus file; and which R function to read the tree? I use Figtree v1.4.4 for Mac, and function read.beast in package treeio to read the nexus tree; it seems to read the CI normally. Cheers, Hien
Juanphg
commented
4 years ago Hello Hien, Yes, is exactly the same data. I also tried to change the lower bounds for "NA" (e.g. NA:58 ) as I saw you explained in a response in google groups, but it didn't read the dates. Then I used just one date (not a range) and the analyses ran without error, but again the CI were not read in figtree. I think is a difference in how trees are written, I saw differences in values under quotation between the file you sent me and the ones I obtained with IQtree. I have used the function read.newick in Phytools and read.nexus in ape, but didn't try read.beast. Tomorrow, when I go back to the PC I will try it and let you know what happens I have used Figtree 1.4.3 and 1.4.4 on Windows.
Cheers,
Juan P.
El mié., 17 de junio de 2020 20:55, Thu-Hien To notifications@github.com escribió:
Hi, is it exactly the same data that you sent me last time? If you did some modifications, could you send me again the input tree and the input date file?
Hien
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tothuhien
commented
4 years ago Hi Juan, Normally read.newick and read.nexus don't read the annotations in nexus file; but read.beast (package treeio) does.
For Figtree, I think there's a bit different between windows and Mac version that I didn't know neither. So if I understand well, when you use Figtree windows, it can read CI value in the tree that I sent you (without quotation between values of CI), but cannot read the one generated by iq-tree (with quotation)? But following @bqminh, we should put quotations between values of CI so that figtree can read it, that's why he put them in. For me, both (with/without quotation) works for my Figtree and the function read.beast. But I prefer without quotation because just like that we can use the feature 'Node Bars' in figtree, which draw the bars of confidence intervals (using CI_height values in the nexus tree). So Minh, could you check again do we really need the quotations in nexus tree? for which version/OS of Figtree?
tothuhien
commented
4 years ago and for the different results of dating you obtained, I'm just wondering if you have outgroups in this case? For some reason that I don't remember, I assumed that 2 taxa Boa_constrictor, Eryx_colubrinus are outgroups and I used them to root your tree. (You can see that in my command I did specify an outgroup file). But it seems that when you run iq-tree you don't specify them as outgroups, so it just automatically detect a root for the tree, which maybe different.
Hien
EricDeveaud
commented
4 years ago IQ-TREE-2.0.6 frsh build with lsd2-1.7.1 compiled using the following: eigen/3.1.2 gcc/4.9.0 cmake/2.8.12.2 openmpi/2.0.1
LDFLAGS="-Wl,-rpath,$GCC_ROOT/lib64 $LDFLAGS" \
cmake -DCMAKE_CXX_COMPILER=c++ \
-DCMAKE_C_COMPILER=gcc \
-DCMAKE_INSTALL_PREFIX=$(EXE) \
-DEIGEN3_INCLUDE_DIR=$$EIGEN_ROOT/include \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DIQTREE_FLAGS=omp \
-DUSE_LSD2=ON \
$(SOFT)/IQ-TREE/IQ-TREE-0.6.2 downloaded the data provided by Juanphg, ie:
https://github.com/Cibiv/IQ-TREE/files/4763848/Juanphg.zip https://github.com/Cibiv/IQ-TREE/files/4766922/IQ.txt
and ran the last command line provided by Juanphg here's the ouput
c6builder:2.0.6/Juanphg > iqtree2 -s allignment.phy -p partitions.txt -te IQ.txt --date Dating_file.txt --date-tip 0 --date-ci 100
IQ-TREE multicore version 2.0.6 for Linux 64-bit built Jun 25 2020
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: c6builder.it.pasteur.fr (AVX, 15 GB RAM)
Command: iqtree2 -s allignment.phy -p partitions.txt -te IQ.txt --date Dating_file.txt --date-tip 0 --date-ci 100
Seed: 311554 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Jun 25 16:59:22 2020
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading partition model file partitions.txt ...
Reading alignment file allignment.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
WARNING: 19 sites contain only gaps or ambiguous characters.
Alignment has 107 sequences with 3652 columns, 2320 distinct patterns
1653 parsimony-informative, 344 singleton sites, 1655 constant sites
Gap/Ambiguity Composition p-value
1 Achalinus_rufescens 37.13% failed 0.00%
2 Afronatrix_anoscopus 8.60% failed 3.08%
3 Aplopeltura_boa 20.62% passed 5.84%
4 Atractaspis_micropholis 13.42% passed 62.73%
5 Azemiops_feae 18.13% passed 92.63%
6 Bitis_arietans 34.01% failed 0.66%
7 Boa_constrictor 11.01% failed 2.06%
8 Bothriechis_schlegelii 25.82% passed 22.84%
9 Buhoma_depressiceps 31.87% passed 14.43%
10 Buhoma_procterae 14.10% failed 3.62%
11 Bungarus_ceylonicus 10.21% failed 0.07%
12 Calamaria_pavimentata 41.81% passed 5.57%
13 Calliophis_melanurus 10.05% passed 24.12%
14 Cerberus_rynchops 20.95% passed 31.74%
15 Coluber_constrictor 9.20% passed 27.32%
16 Compsophis_infralineatus 11.69% failed 0.60%
17 Crotalus_adamanteus 23.63% passed 23.63%
18 Cubophis_cantherigerus 35.57% passed 28.74%
19 Daboia_russelii 9.01% passed 41.78%
20 Dendroaspis_angusticeps 16.68% passed 86.22%
21 Diadophis_punctatus 14.79% passed 98.50%
22 Drymarchon_corais 11.86% passed 6.24%
23 Erpeton_tentaculatum 29.22% passed 59.92%
24 Eryx_colubrinus 34.75% failed 0.28%
25 Gonionotophis_brussauxi 14.10% passed 22.64%
26 Grayia_ornata 29.98% passed 50.39%
27 Helicops_infrataeniatus 29.05% passed 29.76%
28 Hormonotus_modestus 16.87% failed 0.01%
29 Hydrophis_curtus 9.50% passed 65.60%
30 Imantodes_cenchoa 11.04% passed 31.93%
31 Laticauda_colubrina 10.24% failed 2.08%
32 Laticauda_laticaudata 35.90% failed 0.90%
33 Leioheterodon_madagascariensis 12.62% passed 25.08%
34 Madagascarophis_colubrinus 8.49% passed 32.98%
35 Malpolon_monspessulanus 9.31% passed 56.27%
36 Micruroides_euryxanthus 23.71% passed 90.57%
37 Naja_naja 8.76% passed 94.62%
38 Natrix_natrix 12.65% passed 79.09%
39 Nerodia_sipedon 9.31% passed 83.74%
40 Ninia_atrata 29.30% passed 84.40%
41 Ophiophagus_hannah 7.86% passed 54.88%
42 Oxyuranus_microlepidotus 13.14% passed 18.46%
43 Pareas_hamptoni 17.61% passed 7.28%
44 Plagiopholis_styani 57.20% failed 0.00%
45 Psammophis_mossambicus 8.87% passed 8.44%
46 Pseudechis_australis 9.34% failed 4.89%
47 Pseudoxenodon_karlschmidti 42.80% failed 3.83%
48 Rhinocheilus_lecontei 8.79% passed 9.77%
49 Salvadora_hexalepis 21.88% passed 5.36%
50 Scaphiodontophis_annulatus 55.12% failed 2.81%
51 Sibynophis_collaris 10.71% passed 66.94%
52 Simoselaps_anomalus 12.38% passed 47.47%
53 Sinomicrurus_macclellandi 22.18% failed 3.05%
54 Stoliczkia_borneensis 69.50% failed 0.01%
55 Thamnophis_sirtalis 9.34% passed 85.36%
56 Thermophis_baileyi 35.87% failed 2.10%
57 Thermophis_zhaoermii 10.82% passed 16.17%
58 Toxicocalamus_preussi 12.43% passed 43.75%
59 Trimeresurus_stejnegeri 21.25% passed 92.34%
60 Vipera_eriwanensis 22.51% passed 67.89%
61 Xenocalamus_transvaalensis 13.44% passed 65.75%
62 Xenodermus_javanicus 32.86% passed 26.16%
63 IB55595 77.77% passed 15.62%
64 MCP5035 77.77% passed 20.35%
65 MZUSP10808 77.77% passed 9.54%
66 CEPB2301 77.77% passed 14.81%
67 IB55385 77.77% passed 13.30%
68 CEPB2687 77.77% passed 6.40%
69 CEPB2312 77.77% passed 13.28%
70 IVB1757 77.77% passed 14.66%
71 UWIZM2016_22 31.68% failed 1.93%
72 CEPB051 77.77% passed 26.82%
73 RH52446_M50 41.46% passed 76.77%
74 UTAM673 77.79% passed 34.14%
75 CAS231787 31.54% passed 17.57%
76 ROM22835 77.82% passed 5.81%
77 UWIZM2012_4 33.49% passed 13.08%
78 UWIZM2016_24 31.65% passed 17.31%
79 M22 62.35% failed 0.00%
80 f80 40.74% failed 1.91%
81 P 15.85% passed 92.07%
82 CEPB1587 77.77% passed 15.40%
83 CEPB2365 77.77% passed 16.66%
84 GU045453 33.98% passed 44.21%
85 CEPB2289 77.77% failed 4.78%
86 YPX161 66.62% passed 25.23%
87 MPEG19054 77.79% failed 4.06%
88 CAS257629 34.42% passed 17.31%
89 CH5377 64.43% failed 1.02%
90 MHUAR14488 77.77% passed 6.98%
91 WED54125 46.99% failed 0.80%
92 M13 62.38% failed 0.00%
93 CEPB1807 77.77% passed 18.60%
94 KU222205 77.77% passed 25.60%
95 LSUMZH1529 78.07% passed 30.80%
96 QCAZ2584 77.77% passed 24.96%
97 LSUMZH6130 77.88% passed 8.71%
98 MZUSP10809 77.77% passed 7.49%
99 l76 19.22% passed 87.10%
100 l77 19.22% passed 85.66%
101 l5 71.99% failed 0.19%
102 f1 38.83% passed 12.17%
103 f2 17.50% passed 91.21%
104 l2 18.37% passed 87.02%
105 LJV7110 47.62% failed 0.35%
106 Vidal_KU214908 45.45% failed 2.64%
107 FTB2189_449 39.92% failed 0.42%
WARNING: 30 sequences contain more than 50% gaps/ambiguity
**** TOTAL 36.52% 30 sequences failed composition chi2 test (p-value<5%; df=3)
Loading 11 partitions...
Subset Type Seqs Sites Infor Invar Model Name
1 DNA 76 540 232 248 GTR+I+G Subset1
2 DNA 75 561 192 312 GTR+I+G Subset2
3 DNA 80 373 224 125 GTR+I+G Subset3
4 DNA 80 373 112 218 TVM+I+G Subset4
5 DNA 80 372 295 65 TIM+I+G Subset5
6 DNA 98 288 136 135 GTR+I+G Subset6
7 DNA 98 288 70 187 TVM+I+G Subset7
8 98 287 234 44 K81UF+G Subset8
9 DNA 76 190 85 53 HKY+G Subset9
10 DNA 76 190 37 131 K80+G Subset10
11 DNA 76 190 36 137 HKY+G Subset11
Degree of missing data: 0.231
Info: multi-threading strategy over partitions
Reading input tree file IQ.txt ...
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1 funcAbort()
ERROR: 3 ModelMarkov::decomposeRateMatrix()
ERROR: 4 ModelMarkov::init(StateFreqType)
ERROR: 5 ModelDNA::init(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, StateFreqType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
ERROR: 6 ModelDNA::ModelDNA(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, StateFreqType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, PhyloTree*)
ERROR: 7 createModel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ModelsBlock*, StateFreqType, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, PhyloTree*)
ERROR: 8 ModelFactory::ModelFactory(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, PhyloTree*, ModelsBlock*)
ERROR: 9 PartitionModel::PartitionModel(Params&, PhyloSuperTree*, ModelsBlock*)
ERROR: 10 PartitionModelPlen::PartitionModelPlen(Params&, PhyloSuperTreePlen*, ModelsBlock*)
ERROR: 11 IQTree::initializeModel(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ModelsBlock*)
ERROR: 12 runTreeReconstruction(Params&, IQTree*&)
ERROR: 13 runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 14 main()
ERROR: 15 __libc_start_main()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: partitions.txt.log
ERROR: *** Alignment files (if possible)
zsh: segmentation fault (core dumped) iqtree2 -s allignment.phy -p partitions.txt -te IQ.txt --date Dating_file.txt
and for the different results of dating you obtained, I'm just wondering if you have outgroups in this case? For some reason that I don't remember, I assumed that 2 taxa Boa_constrictor, Eryx_colubrinus are outgroups and I used them to root your tree. (You can see that in my command I did specify an outgroup file). But it seems that when you run iq-tree you don't specify them as outgroups, so it just automatically detect a root for the tree, which maybe different.
Hien
Hello, Sorry again for my late answer. I reran the analyses, specifying the outgroup also in a different file, in the lsd analysis. The analyses ran without problems this time. I ran Iqtree in Windows 10 and Ubuntu 19 and in both got the same results. Nevertheless, I'm having the same problems with the trees with Figtree 1.4.4 in both OS, cant use the node bars. I also opened the tree in R with treeio as you said, using the commands read.beast and read.iqtree, and trees were imported. Nevertheless, I wasn't able to plot them using additional packages, such as phytools, ape, but it could be because my skills with R are limited. But, I must say, that in the past, I haven't had problems manipulating trees coming from IQ, Beast and Raxml. These were the commands I used: qtree2 -s allignment.phy -p partitions.txt -st DNA -B 5000 -T 4 --date Dating_file.txt --date-ci 100 --date-tip 0 --date-options "-g OG.txt" -o Boa_constrictor,Eryx_colubrinus. The OG.txt file is a file just with the outgroups.
Cheers, JP
Elisa-noc
commented
1 year ago Goodmornig everyone, Sorry to barge into this conversation but I’m new on IQTREE and I need some help. I don’t understand why although in my Date file there are fossil dates (example 50 Mya), at node ages on Figtree I see a decimal number...even if I open the example that you have sent in this conversation the same thing happens to me. I’m desperate! Someone could help me? Cheers Elisa
tothuhien
commented
1 year ago Hi @Elisa-noc , I'm not sure what your problem is. Why node ages as decimal number is a problem for you, could you explain a bit more?
Elisa-noc
commented
1 year ago Hi tothuien, Thanks first for the prompt response and sorry if I did not explain well. I have a problem with dating my nodes. For example, the highlighted node is dated - 20 (Mya) on my data_file, but when I open tree with Figtree, it turns out 2.22. I attach figure. I don’t understand what I’m doing wrong. Maybe it is a stupid mistake...
Thank you in advance!
Elisa
Elisa-noc
commented
1 year ago So, my question in simple words: what do I have to do to see the node a value of 40 (for 40 mya of MRCA) and not 0.4? Thank you again
tothuhien
commented
1 year ago Hi, it could be either your tree was not correctly dated, or the dating was correct but you didn’t select the correct values to see for node labels. In order to know what was the issue, l need to know your dated nexus tree and the command line you have used to generate the dated tree.
Elisa-noc
commented
1 year ago Hi, I did another test and in fact the dating now makes more sense, but I still don’t understand why for example the most ancestral node is 0.8 and not 80. I wonder if I’m wrong about the dating process, because the results are strange...
My script: bin\iqtree2 -s provacorta.fasta -st DNA -p part_and_sub.PARTITIONS -B 1000 -T 4 --date DATE.cortissima.txt --date-tip 0
My DATE.FILE Date.cortissima.txt
My timetree
Thank you in advance
tothuhien
commented
1 year ago Could you try at the menu 'Node Labels' -> 'Display' : select 'date' instead of 'Node ages'?
Elisa-noc
commented
1 year ago I searched but unfortunately there is no such option on my figtree
tothuhien
commented
1 year ago Did you look at there (red rectangle in this figure)? Which options do you have at 'Display'? Could you give me the text file of the nexus tree instead of the figure?
tothuhien
commented
1 year ago Your tree does not look like a dated tree. You should have another tree in nexus format which contains date information. Could you check again? If you don’t have that kind if tree, then maybe the dating step was not finished properly. Could you give me the log file so we can see what happened?
Elisa-noc
commented
1 year ago Thank you for your time... For the nexus tree is the same. prova_file_nexus.txt Here my file log prova_iqtree.log
tothuhien
commented
1 year ago It’s not of nexus format neither, it’s still of newick format. Didn’t you get another type of tree?
Elisa-noc
commented
1 year ago Maybe this one? prova.timetree.txt
tothuhien
commented
1 year ago Yes that is the nexus dated tree. Have you tried to open it with figtree ?
Elisa-noc
commented
1 year ago yes and it works! Thank you very much Thu-Hien and sorry to waste your time
tothuhien
commented
1 year ago No problem 😉
juliadupin
commented
1 year ago Hi all, I am getting a segmentation fault as well when using IQ-TREE multicore version 2.2.2.3 and the command
iqtree2 -s Concat_f.fasta -st DNA --date dates2.txt -te concat_nonodelabel.tree -sp partitions.txt.best_scheme.nex --date-ci 100 --date-options -g outgroups.txt --clock-sd 0.5 --keep-ident -pre oleaceae_iqtree_dated --date-tip 0
... --- Start phylogenetic dating --- Reading date file dates2.txt ... 7 dates extracted Building time tree by least-square dating (LSD) with command: lsd -i oleaceae_iqtree_dated.timetree.subst -s 120057 -o oleaceae_iqtree_dated.timetree -f 100 -q 0.5 -r a -d oleaceae_iqtree_dated.timetree.date -z 0 -g outgroups.txt
TREE 1 *PROCESSING: Reading the tree ... Collapse 13 (over 398) internal branches having branch length <= 4.16e-06 (settable via option -l) ERROR: STACK TRACE FOR DEBUGGING: ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: oleaceae_iqtree_dated.log ERROR: Alignment files (if possible) /var/spool/slurm/d/job45993413/slurm_script: line 22: 63053 Segmentation fault /home/gbesnard/iqtree-2.2.2.3-Linux/bin/iqtree2 -s Concat_f.fasta -st DNA --date dates2.txt -te concat_nonodelabel.tree -sp partitions.txt.best_scheme.nex --date-ci 100 --date-options "-g outgroups.txt" --clock-sd 0.5 --keep-ident -pre oleaceae_iqtree_dated --date-tip 0
I wanted to see if the politomies could be the issue, so I ran
Command: /home/gbesnard/iqtree-2.2.2.3-Linux/bin/iqtree2 -s Concat_f.fasta -st DNA --date dates2.txt -te concat_nonodelabel.tree -sp partitions.txt.best_scheme.nex --date-ci 100 --date-options -l 1.0e-07 -g outgroups.txt --clock-sd 0.5 --keep-ident -pre oleaceae_iqtree_dated --date-tip 0
but still got the error:
TREE 1 *PROCESSING: Reading the tree ... Collapse 0 (over 398) internal branches having branch length <= 1e-07 (settable via option -l) ERROR: STACK TRACE FOR DEBUGGING: ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: oleaceae_iqtree_dated.log ERROR: Alignment files (if possible) /var/spool/slurm/d/job46000118/slurm_script: line 20: 60163 Segmentation fault /home/gbesnard/iqtree-2.2.2.3-Linux/bin/iqtree2 -s Concat_f.fasta -st DNA --date dates2.txt -te concat_nonodelabel.tree -sp partitions.txt.best_scheme.nex --date-ci 100 --date-options "-l 1.0e-07 -g outgroups.txt" --clock-sd 0.5 --keep-ident -pre oleaceae_iqtree_dated --date-tip 0
Could anyone help me out here? What could be causing this error? I will happily share log and alignment files.
Thank you!!
Julia
tothuhien
commented
1 year ago Hi Julia, It could be a bug of the program. It would be useful to have the input data to detect where the error comes from. Could you provide the alignments with the date file and also outgroup? Hien
juliadupin
commented
1 year ago Hi Hien,
thank you for your quick reply.
I realized I made a mistake and didn't make the outgroup file available when running those analyses. I have re-launched it and it is currently running (but not yet at the dating step).
That being said, at first, I tried setting the outgroups through iqtree, using the command -o but it would not work (it seemed to ignore it completely, but it didn't return an error either) (I was using v2.1.3). That is why I changed to using the argument -g under LSD2. I am a bit surprised it didn't return an error when it didn't find the outgroups file.
Once my new analyses finish running I'll let you know if it went well.
Thanks!
Julia
juliadupin
commented
1 year ago Hi Hien,
the new run didn't work either. The error has changed though, from a segmentation fault to a crash with signal aborted.
TREE 1 *PROCESSING: Reading the tree ... Collapse 0 (over 398) internal branches having branch length <= 1e-07 (settable via option -l) double free or corruption (!prev) ERROR: STACK TRACE FOR DEBUGGING: ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: For bug report please send to developers: ERROR: Log file: oleaceae_iqtree_dated.log ERROR: Alignment files (if possible) /var/spool/slurm/d/job46017208/slurm_script: line 20: 12752 Aborted /home/gbesnard/iqtree-2.2.2.3-Linux/bin/iqtree2 -s Concat_f.fasta -st DNA --date dates2.txt -te concat_nonodelabel.tree -sp partitions.txt.best_scheme.nex --date-ci 100 --date-options "-l 1.0e-07 -g outgroups.txt" --clock-sd 0.5 --keep-ident -pre oleaceae_iqtree_dated --date-tip 0
how could I send you my files directly? Thanks!
Julia
tothuhien
commented
1 year ago Hi, you can send them to my email tothuhien@gmail.com Cheers, Hien
Hello, I'm exploring the dating option with my data using the input as follows: \iqtree2.exe -s lemni_realligned_20200602_woalti.phy -p best_scheme_realligned_PF_20200602.txt -t PARS -B 5000 --date dating_iq.txt --date-tip 0 it runs normally, write the tree with the UFB support, but when starts dating, I get the following message:
--- Start phylogenetic dating --- Reading date file dating_iq.txt ... 117 dates extracted Building time tree by least-square dating (LSD) with command: lsd -i best_scheme_realligned_PF_20200602.txt.timetree.subst -s 3652 -o best_scheme_realligned_PF_20200602.txt.timetree -r a -d best_scheme_realligned_PF_20200602.txt.timetree.date
TREE 1 *PROCESSING: Reading the tree ... Collapse 3 (over 106) internal branches having branch length <= 0.000 (settable via option -l) Parameter to adjust variances was set to 0.039 (settable via option -b) ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: best_scheme_realligned_PF_20200602.txt.log ERROR: Alignment files (if possible)
Thanks in advance for your help and for IQ,
Cheers, Juan Pablo Hurtado juanphg@gmail.com