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Gene tree - species tree reconciliation from gene tree distributions
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
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.
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
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.
This change (deprecation of --per-family-rates
, etc):
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
.
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.
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