benoitmorel / alerax Goto Github PK

This change (deprecation of --per-family-rates, etc):

d873d0b

breaks these tests:

https://github.com/BenoitMorel/AleRax/blob/main/tests/run_alerax_tests.py#L110-L113

Thanks!

P.S. For users of Slurm, it would be nice if the tests had an option to use srun instead of mpiexec.

Hi Benoit,

Thank you for developing this !

I tried to use alerax to do the gene tree reconcilation, the ccps were generated fine, but then I ran into an error :

[01:54:44] Remaining families: 27451
[01:54:44] Initializing starting species tree...
[01:54:44] Remaining families: 27451
[01:54:44] Initializing starting species tree...
terminate called after throwing an instance of 'LibpllException'
what(): Error while reading rooted tree from file alerax_output/species_trees/starting_species_tree.newick.
Error name: NO_SEMICOLON.
Error help message: The newick string should end with a semicolon.
The parsing error was detected at character 4294967295.

I checked the starting species tree in the output folder, it has semicolon and everything, but the running process was halted.
the nwk looks like this
((4:1.000000,98:1.000000)Node_4_98_0:1.000000,((14:1.000000,(21:1.000000,(55:1.000000,(70:1.000000,(25:1.000000,(10:1.000000,64:1.000000)Node_10_64_0:1.000000)Node_25_10_0:1.000000)Node_70_25_0:1.000000)Node_55_70_0:1.000000)Node_21_55_0:1.000000)Node_14_21_0:1.000000,(((78:1.000000,(51:1.000000,75:1.000000)Node_51_75_0:1.000000)Node_78_51_0:1.000000,((31:1.000000,76:1.000000)Node_31_76_0:1.000000,(37:1.000000,39:1.000000)Node_37_39_0:1.000000)Node_31_37_0:1.000000)Node_78_31_0:1.000000,(((2:1.000000,100:1.000000)Node_2_100_0:1.000000,(79:1.000000,(77:1.000000,86:1.000000)Node_77_86_0:1.000000)Node_79_77_0:1.000000)Node_2_79_0:1.000000,(63:1.000000,(((72:1.000000,81:1.000000)Node_72_81_0:1.000000,((30:1.000000,80:1.000000)Node_30_80_0:1.000000,(84:1.000000,(83:1.000000,85:1.000000)Node_83_85_0:1.000000)Node_84_83_0:1.000000)Node_30_84_0:1.000000)Node_72_30_0:1.000000,(((46:1.000000,47:1.000000)Node_46_47_0:1.000000,((59:1.000000,60:1.000000)Node_59_60_0:1.000000,((38:1.000000,73:1.000000)Node_38_73_0:1.000000,(66:1.000000,(61:1.000000,74:1.000000)Node_61_74_0:1.000000)Node_66_61_0:1.000000)Node_38_66_0:1.000000)Node_59_38_0:1.000000)Node_46_59_0:1.000000,(((((8:1.000000,58:1.000000)Node_8_58_0:1.000000,(15:1.000000,71:1.000000)Node_15_71_0:1.000000)Node_8_15_0:1.000000,(93:1.000000,((26:1.000000,50:1.000000)Node_26_50_0:1.000000,(23:1.000000,(29:1.000000,49:1.000000)Node_29_49_0:1.000000)Node_23_29_0:1.000000)Node_26_23_0:1.000000)Node_93_26_0:1.000000)Node_8_93_0:1.000000,(((53:1.000000,(44:1.000000,(43:1.000000,82:1.000000)Node_43_82_0:1.000000)Node_44_43_0:1.000000)Node_53_44_0:1.000000,((89:1.000000,(45:1.000000,94:1.000000)Node_45_94_0:1.000000)Node_89_45_0:1.000000,(96:1.000000,(16:1.000000,(12:1.000000,(9:1.000000,91:1.000000)Node_9_91_0:1.000000)Node_12_9_0:1.000000)Node_16_12_0:1.000000)Node_96_16_0:1.000000)Node_89_96_0:1.000000)Node_53_89_0:1.000000,((24:1.000000,(35:1.000000,(52:1.000000,(18:1.000000,(17:1.000000,19:1.000000)Node_17_19_0:1.000000)Node_18_17_0:1.000000)Node_52_18_0:1.000000)Node_35_52_0:1.000000)Node_24_35_0:1.000000,((32:1.000000,34:1.000000)Node_32_34_0:1.000000,(57:1.000000,(33:1.000000,(65:1.000000,67:1.000000)Node_65_67_0:1.000000)Node_33_65_0:1.000000)Node_57_33_0:1.000000)Node_32_57_0:1.000000)Node_24_32_0:1.000000)Node_53_24_0:1.000000)Node_8_53_0:1.000000,((36:1.000000,((11:1.000000,40:1.000000)Node_11_40_0:1.000000,((5:1.000000,(6:1.000000,(7:1.000000,87:1.000000)Node_7_87_0:1.000000)Node_6_7_0:1.000000)Node_5_6_0:1.000000,(27:1.000000,(28:1.000000,(13:1.000000,62:1.000000)Node_13_62_0:1.000000)Node_28_13_0:1.000000)Node_27_28_0:1.000000)Node_5_27_0:1.000000)Node_11_5_0:1.000000)Node_36_11_0:1.000000,((((41:1.000000,92:1.000000)Node_41_92_0:1.000000,(42:1.000000,(22:1.000000,90:1.000000)Node_22_90_0:1.000000)Node_42_22_0:1.000000)Node_41_42_0:1.000000,((68:1.000000,(56:1.000000,88:1.000000)Node_56_88_0:1.000000)Node_68_56_0:1.000000,((20:1.000000,69:1.000000)Node_20_69_0:1.000000,(48:1.000000,(54:1.000000,95:1.000000)Node_54_95_0:1.000000)Node_48_54_0:1.000000)Node_20_48_0:1.000000)Node_68_20_0:1.000000)Node_41_68_0:1.000000,((106:1.000000,107:1.000000)Node_106_107_0:1.000000,((102:1.000000,(108:1.000000,109:1.000000)Node_108_109_0:1.000000)Node_102_108_0:1.000000,(101:1.000000,(((1:1.000000,112:1.000000)Node_1_112_0:1.000000,(103:1.000000,104:1.000000)Node_103_104_0:1.000000)Node_1_103_0:1.000000,((110:1.000000,(3:1.000000,111:1.000000)Node_3_111_0:1.000000)Node_110_3_0:1.000000,((113:1.000000,114:1.000000)Node_113_114_0:1.000000,(97:1.000000,(99:1.000000,105:1.000000)Node_99_105_0:1.000000)Node_97_99_0:1.000000)Node_113_97_0:1.000000)Node_110_113_0:1.000000)Node_1_110_0:1.000000)Node_101_1_0:1.000000)Node_102_101_0:1.000000)Node_106_102_0:1.000000)Node_41_106_0:1.000000)Node_36_41_0:1.000000)Node_8_36_0:1.000000)Node_46_8_0:1.000000)Node_72_46_0:1.000000)Node_63_72_0:1.000000)Node_2_63_0:1.000000)Node_78_2_0:1.000000)Node_14_78_0:1.000000)Node_4_14_0:1.000000;

Could you identify where the problem is?

Best,
Mia

Hi Benoit,

Thanks for developing this tool. I tired to use --species-categories and --fraction-missing option in my analysis, but found that these two options are shown as "--speciies-categories" and " --fraction-missing-file" in the help message. See below.

Arguments:
https://github.com/BenoitMorel/AleRax/blob/1d7ea777575f4954b43541e21e3721247389638d/src/ale/AleArguments.cpp#L102C1-L104C48

Help:
https://github.com/BenoitMorel/AleRax/blob/1d7ea777575f4954b43541e21e3721247389638d/src/ale/AleArguments.cpp#L262C1-L265C71

Hello, I'm trying to run an analysis with AleRax, but it crashes on a segfault very early in the process.

You will find attached a minimal example to reproduce; you just need to launch run.sh within the targz-ed folder.

alerax-bugreport.tar.gz

Thank you for developing this tool!

I'm trying to compile the source code on my Mac. I'm encountering errors when it gets to AleEvaluator.cpp and AleOptimizer.cpp. Below are some of the error messages I got.

/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/c++/v1/algorithm:3877:20: error: no matching function for call to '__sort3'
    unsigned __r = _VSTD::__sort3<_Compare>(__x1, __x2, __x3, __c);
                   ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/c++/v1/__config:856:15: note: expanded from macro '_VSTD'
#define _VSTD std::_LIBCPP_ABI_NAMESPACE
              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/c++/v1/algorithm:4098:20: note: in instantiation of function template specialization 'std::__sort4<std::__less<ScoredString> &, ScoredString *>' requested here
            _VSTD::__sort4<_Compare>(__first, __first+1, __first+2, --__last, __comp);

I'm using gcc version 13.0.0 and cmake version 3.27.7. Any pointers would be much appreciated. Thanks in advance.

I got an error when trying to git clone the repo as per the instructions ( git clone --recursive https://github.com/BenoitMorel/AleRax)

fatal: remote error: upload-pack: not our ref 157a236f12fd9218305c9937006d3ee8e3c3ee4b fatal: Fetched in submodule path 'ext/GeneRaxCore', but it did not contain 157a236f12fd9218305c9937006d3ee8e3c3ee4b. Direct fetching of that commit failed. fatal:

It seems to have to do with the GeneRax submodule. I've also attempted to git clone without the --recursive which works fine, and then do git submodule init and then fetch the GeneRax submodule myself, but at the step of git submodule update I encounter the same error