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When dating, IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT #145

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Juanphg opened this issue Jun 3, 2020 · 45 comments
Open

When dating, IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT #145

Juanphg opened this issue Jun 3, 2020 · 45 comments

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@Juanphg
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Juanphg commented Jun 3, 2020

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
@bqminh
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bqminh commented Jun 4, 2020

Can you pls provide the date file?
Is the date in the right format YYYY-MM-DD?

@Juanphg
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Juanphg commented Jun 4, 2020 via email

@bqminh
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bqminh commented Jun 4, 2020

Can you pls try v2.0.6, from the release tab. It fixes a few bugs in LSD2

@bqminh
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bqminh commented Jun 4, 2020

https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6

@Juanphg
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Juanphg commented Jun 5, 2020 via email

@bqminh
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bqminh commented Jun 10, 2020

@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
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Juanphg commented Jun 11, 2020

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
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tothuhien commented Jun 11, 2020 •
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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
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Juanphg commented Jun 11, 2020 via email

@tothuhien
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Hi, could you attache the file again? I don't see it.

@Juanphg
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Juanphg commented Jun 11, 2020

Here it goes again. I forgot that .tre files are not accepted here.
IQ.txt

@tothuhien
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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:

  • Dating results:
    rate 0.00554891, tMRCA -94.216
  • Results with confidence intervals:
    rate 0.00554891 [0.00513215; 0.00633979], tMRCA -94.216 [-110.319; -83.4702]

and the
dated tree

@bqminh
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bqminh commented Jun 12, 2020

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
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Juanphg commented Jun 12, 2020 •
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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

partitions.txt.log.txt

Thanks a lot,
Cheers

@tothuhien
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Hi, did you forget to set tips date = 0 (--date-tip 0) ?

Hien

@Juanphg
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Juanphg commented Jun 15, 2020

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:

  • 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.
    *RESULTS:
  • Dating results:
    rate 0.00510251, tMRCA -80.0462
  • Results with confidence intervals:
    rate 0.00510251 [0.00480289; 0.00547235], tMRCA -80.0462 [-89.7245; -73.0599]

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
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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
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tothuhien commented Jun 17, 2020 •
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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
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Juanphg commented Jun 17, 2020 via email

@tothuhien
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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
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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
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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

@Juanphg
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Juanphg commented Jun 26, 2020 •
edited
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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

@BensonPH BensonPH mentioned this issue Jul 2, 2021
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@Elisa-noc
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Elisa-noc commented Dec 7, 2022 •
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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
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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
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Elisa-noc commented Dec 9, 2022 •
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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
Node ages

@Elisa-noc
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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
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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
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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
timetree

Thank you in advance

@tothuhien
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Could you try at the menu 'Node Labels' -> 'Display' : select 'date' instead of 'Node ages'?

@Elisa-noc
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I searched but unfortunately there is no such option on my figtree
Figtree

@tothuhien
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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?
207323797-b3d5f728-ea47-4f98-8f75-ba51cc3441fc

@Elisa-noc
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Yes, of course
I don't have date as an option.
prova.txt

@tothuhien
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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
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Thank you for your time...
For the nexus tree is the same.
prova_file_nexus.txt
Here my file log
prova_iqtree.log

@tothuhien
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It’s not of nexus format neither, it’s still of newick format. Didn’t you get another type of tree?

@Elisa-noc
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Maybe this one?
prova.timetree.txt

@tothuhien
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Yes that is the nexus dated tree. Have you tried to open it with figtree ?

@Elisa-noc
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yes and it works!
Thank you very much Thu-Hien and sorry to waste your time

@tothuhien
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No problem 😉

@juliadupin
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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
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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
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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
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juliadupin commented Mar 29, 2023 •
edited
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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
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Hi, you can send them to my email tothuhien@gmail.com
Cheers,
Hien

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6 participants
@juliadupin @EricDeveaud @tothuhien @bqminh @Juanphg @Elisa-noc