Error - IQtree 1.6 beta - segmentation fault evaluating set of user trees.

[Filipe Romero]

Hi Minh!

I'm currently using IQtree 1.6beta to evaluate a set of trees and perform tests.
I used the following command:

iqtree-beta -nt AUTO -m GTR+G8 -s cat_info_10.txt -z trees_AU.txt -au -zb 10000 -n 0 -t PARS -redo

and got the following error:


Reading trees in trees_AU.txt ...
4 trees detected
Note: 6392.079 MB of RAM required!
Creating 10000 bootstrap replicates...
done
Tree 1(((((Erinaceus:0.1745237044,Sorex:0.2123707052):0.0146538515,((Felis:0.0640998637,((Ailuropoda:0.0384655869,Mustela:0.0604338906):0.0121143955,Canis:0.0566375420):0.0121906200):0.0346157274,((Sus:0.0989642703,((Ovis:0.0268384785,Bos:0.0225912222):0.0566010793,Tursiops:0.0421358605):0.0095212538):0.0060156736,Vicugna:0.0688506996):0.0251339871,(Myotis:0.0857035395,Pteropus:0.0758444032):0.0210267830,Equus:0.0739209867):0.0047176272):0.0129892508,(((Ictidomys:0.1070741043,(Dipodomys:0.1469297988,(Mus:0.0446358055,Rattus:0.0872259022):0.1463703313):0.0121102826,Cavia:0.1593726991):0.0175789416,(Oryctolagus:0.0862063360,Ochotona:0.1297142984):0.0630468698):0.0088071391,(((((Chlorocebus:0.0093667256,(Macaca:0.0121305428,Papio:0.0070306440):0.0021163528):0.0145466296,((((Homo:0.0037169400,Pan:0.0048646410):0.0017183107,Gorilla:0.0152850835):0.0047783353,Pongo:0.0124131166):0.0018638511,Nomascus:0.0168137623):0.0057299193):0.0113115297,Callithrix:0.0508825935):0.0396326873,Tarsius:0.0922282779):0.0067265370,(Otolemur:0.0862547058,Microcebus:0.0671339891):0.0190400234):0.0118685991,Tupaia:0.1389549475):0.0130659695):0.0125083818,((Echinops:0.1737176931,(Loxodonta:0.0875451617,Procavia:0.0946010031):0.0143871869):0.0305052860,(Choloepus:0.0712954745,Dasypus:0.0971376278):0.0450769268):0.0037182121):0.1765373331,((Sarcophilus:0.1046010521,Macropus:0.0790856616):0.0158178363,Monodelphis:0.0833542182):0.1694785632,Ornithorhynchus:0.3433177094);
new_tree_lh: -3028959.2726053940   tree_lh: -2938367.8002452487
(((((Erinaceus:0.1745237044,Sorex:0.2123707052):0.0146538515,((Felis:0.0640998637,((Ailuropoda:0.0384655869,Mustela:0.0604338906):0.0121143955,Canis:0.0566375420):0.0121906200):0.0346157274,((Sus:0.0989642703,((Ovis:0.0268384785,Bos:0.0225912222):0.0566010793,Tursiops:0.0421358605):0.0095212538):0.0060156736,Vicugna:0.0688506996):0.0251339871,(Myotis:0.0857035395,Pteropus:0.0758444032):0.0210267830,Equus:0.0739209867):0.0047176272):0.0129892508,(((Ictidomys:0.1070741043,(Dipodomys:0.1469297988,(Mus:0.0446358055,Rattus:0.0872259022):0.1463703313):0.0121102826,Cavia:0.1593726991):0.0175789416,(Oryctolagus:0.0862063360,Ochotona:0.1297142984):0.0630468698):0.0088071391,(((((Chlorocebus:0.0093667256,(Macaca:0.0121305428,Papio:0.0070306440):0.0021163528):0.0145466296,((((Homo:0.0037169400,Pan:0.0048646410):0.0017183107,Gorilla:0.0152850835):0.0047783353,Pongo:0.0124131166):0.0018638511,Nomascus:0.0168137623):0.0057299193):0.0113115297,Callithrix:0.0508825935):0.0396326873,Tarsius:0.0922282779):0.0067265370,(Otolemur:0.0862547058,Microcebus:0.0671339891):0.0190400234):0.0118685991,Tupaia:0.1389549475):0.0130659695):0.0125083818,((Echinops:0.1737176931,(Loxodonta:0.0875451617,Procavia:0.0946010031):0.0143871869):0.0305052860,(Choloepus:0.0712954745,Dasypus:0.0971376278):0.0450769268):0.0037182121):0.1765373331,((Sarcophilus:0.1046010521,Macropus:0.0790856616):0.0158178363,Monodelphis:0.0833542182):0.1694785632,Ornithorhynchus:0.3433177094);ERROR: phylotree.cpp:2574: virtual double PhyloTree::optimizeAllBranches(int, double, int): Assertion `fabs(new_tree_lh-tree_lh) < max_delta_lh' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: cat_info_10.txt.log
ERROR: ***    Alignment files (if possible)



I also found an error trying to do this in a previous version and without the '-t PARS' option:


Reading trees in trees_AU.txt ...
4 trees detected
Note: 6392.079 MB of RAM required!
Creating 10000 bootstrap replicates...
done
Tree 1new_tree_lh: -3016015.822   tree_lh: -2953504.505
STACK TRACE FOR DEBUGGING:

*** IQ-TREE CRASHES WITH SIGNAL ABORTED
*** For bug report please send to developers:
***    Log file: cat_info_10.txt.log
***    Alignment files (if possible)





I'm sending both log files. I renamed the log file of the previous version to 'cat_info_10_old.txt' . I would like to share the alignment and the trees via personal email. May I?
The trees contain some polytomies and I think this may be related to the problem.


Thanks in advance,

Filipe Moreira.

[Bui Quang Minh]

Hi Filipe,

Thanks for the report. Does it work when user trees have no polytomy?

Nevertheless, please send me the alignment and trees via my personal email.

Cheers, Minh

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<cat_info_10.txt.log><cat_info_10_old.txt.log>

--

Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at

[Filipe Romero]

Hi, Mihn.

I actually have not tested this yet. I will do this right now.
I'm sending the files via personal email.

Cheers,

Filipe.

[Filipe Romero]

Hi, Minh.

I'm trying again with different alignments and I get the following error:

Reading trees in trees_AU.txt ...
4 trees detected

Note: 5172.467 MB of RAM required!

Creating 10000 bootstrap replicates...
done

Tree 1 / LogL: -2528621.856
Tree 2 / LogL: -2528651.592
Tree 3 / LogL: -2528637.634
Tree 4(Loxodonta:0.1000000000,Procavia:0.1000000000,(Echinops:0.1000000000,((Choloepus:0.1000000000,Dasypus:0.1000000000):0.1000000000,(((Sarcophilus:0.1000000000,Macropus:0.1000000000):0.1000000000,Monodelphis:0.1000000000):0.1000000000,Ornithorhynchus:0.1000000000):0.1000000000,((((Ictidomys:0.1000000000,(Dipodomys:0.1000000000,(Mus:0.1000000000,Rattus:0.1000000000):0.1000000000):0.1000000000,Cavia:0.1000000000):0.1000000000,(Oryctolagus:0.1000000000,Ochotona:0.1000000000):0.1000000000):0.1000000000,(((((Chlorocebus:0.1000000000,(Macaca:0.1000000000,Papio:0.1000000000):0.1000000000):0.1000000000,((((Homo:0.1000000000,Pan:0.1000000000):0.1000000000,Gorilla:0.1000000000):0.1000000000,Pongo:0.1000000000):0.1000000000,Nomascus:0.1000000000):0.1000000000):0.1000000000,Callithrix:0.1000000000):0.1000000000,Tarsius:0.1000000000):0.1000000000,(Otolemur:0.1000000000,Microcebus:0.1000000000):0.1000000000):0.1000000000,Tupaia:0.1000000000):0.1000000000,(((Felis:0.1000000000,((Ailuropoda:0.1000000000,Mustela:0.1000000000):0.1000000000,Canis:0.1000000000):0.1000000000):0.1000000000,((Sus:0.1000000000,((Ovis:0.1000000000,Bos:0.1000000000):0.1000000000,Tursiops:0.1000000000):0.1000000000):0.1000000000,Vicugna:0.1000000000):0.1000000000,(Myotis:0.1000000000,Pteropus:0.1000000000):0.1000000000,Equus:0.1000000000):0.1000000000,(Erinaceus:0.1000000000,Sorex:0.1000000000):0.1000000000):0.1000000000):0.1000000000):0.1000000000):0.1000000000);
new_tree_lh: -2657594.9131249934   tree_lh: -2672354.5610774178
(Loxodonta:0.1000000000,Procavia:0.1000000000,(Echinops:0.1000000000,((Choloepus:0.1000000000,Dasypus:0.1000000000):0.1000000000,(((Sarcophilus:0.1000000000,Macropus:0.1000000000):0.1000000000,Monodelphis:0.1000000000):0.1000000000,Ornithorhynchus:0.1000000000):0.1000000000,((((Ictidomys:0.1000000000,(Dipodomys:0.1000000000,(Mus:0.1000000000,Rattus:0.1000000000):0.1000000000):0.1000000000,Cavia:0.1000000000):0.1000000000,(Oryctolagus:0.1000000000,Ochotona:0.1000000000):0.1000000000):0.1000000000,(((((Chlorocebus:0.1000000000,(Macaca:0.1000000000,Papio:0.1000000000):0.1000000000):0.1000000000,((((Homo:0.1000000000,Pan:0.1000000000):0.1000000000,Gorilla:0.1000000000):0.1000000000,Pongo:0.1000000000):0.1000000000,Nomascus:0.1000000000):0.1000000000):0.1000000000,Callithrix:0.1000000000):0.1000000000,Tarsius:0.1000000000):0.1000000000,(Otolemur:0.1000000000,Microcebus:0.1000000000):0.1000000000):0.1000000000,Tupaia:0.1000000000):0.1000000000,(((Felis:0.1000000000,((Ailuropoda:0.1000000000,Mustela:0.1000000000):0.1000000000,Canis:0.1000000000):0.1000000000):0.1000000000,((Sus:0.1000000000,((Ovis:0.1000000000,Bos:0.1000000000):0.1000000000,Tursiops:0.1000000000):0.1000000000):0.1000000000,Vicugna:0.1000000000):0.1000000000,(Myotis:0.1000000000,Pteropus:0.1000000000):0.1000000000,Equus:0.1000000000):0.1000000000,(Erinaceus:0.1000000000,Sorex:0.1000000000):0.1000000000):0.1000000000):0.1000000000):0.1000000000):0.1000000000);ERROR: phylotree.cpp:2574: virtual double PhyloTree::optimizeAllBranches(int, double, int): Assertion `fabs(new_tree_lh-tree_lh) < max_delta_lh' failed.

ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: pars.cat_info_5.phy.log

ERROR: ***    Alignment files (if possible)

--

I think this error message might be useful.

Cheers,

Filipe.

[Bui Quang Minh]

Dear Filipe,

Am I right that this problem is still related to (or the same as) the one you sent not so long ago, right? I will have a look, was just too busy during the past weeks.

Cheers, Minh

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