Error message. The newick string should end with a semicolon.

[Mia1349]

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

[BenoitMorel]

Hi Mia, The tree looks fine. Is that exactly the tree in alerax_output/species_trees/starting_species_tree.newick ? Could you please send me a small subset of the families (one or two families with the tree distributions, the mapping file, and the input species tree) such that I can reproduce on my laptop? Thanks! Benoit Le ven. 12 avr. 2024 à 03:01, Hongyue ***@***.***> a écrit :

…

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 — Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UMED645FPK6KBDYDPDY44XAJAVCNFSM6AAAAABGDH7TOWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTQOBUGI2TEMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Mia1349]

Hi Benoit,

I've been testing a subset of gene families, and I encountered an issue when using mpiexec for execution. The program runs fine on a single core, but fails with the following mpiexec command:

"mpiexec -np 8 alerax -f mapping.txt -s rooted_C60_fungi.treefile.renamed --fraction-missing-file fraction_missing-1.txt
"

Could there be an issue with the command line syntax, or is it something else?

While running the analysis on a single core does work, it is considerably slow. Processing over 27,000 gene families took about three weeks to complete.

Additionally, I'm struggling to interpret the output files. My objective is to reconstruct the gene family content in ancestral nodes. With ALE, some larger gene families had to be eliminated due to numerical issues. I assume alerax can handle this now? Could you guide me on how to extract the necessary information from the result files?

Thank you very much for your assistance.

Best regards,

Mia
test_set.tar.gz

[BenoitMorel]

Hi Mia, I don't know, it seems to work on my machine with your command. Maybe you forgot to remove the output file and there is some kind of conflict with a previous run? Does it fail with the exact dataset that you sent me? Do you see anything else weird with the logs in the console (like duplicated logs, which could show a problem with the mpi installation. Can you run the install.sh script again and send me all the installation logs that appear in the console? AleRax should be able to handle the files that ALE failed to analyze due to numerical issues, yes. Regarding the output files, do you have any specific question? Also, have you checked the wiki? Best, Benoit Le mar. 30 avr. 2024 à 04:38, Hongyue ***@***.***> a écrit :

…

Hi Benoit, I've been testing a subset of gene families, and I encountered an issue when using mpiexec for execution. The program runs fine on a single core, but fails with the following mpiexec command: "mpiexec -np 8 alerax -f mapping.txt -s rooted_C60_fungi.treefile.renamed --fraction-missing-file fraction_missing-1.txt " Could there be an issue with the command line syntax, or is it something else? While running the analysis on a single core does work, it is considerably slow. Processing over 27,000 gene families took about three weeks to complete. Additionally, I'm struggling to interpret the output files. My objective is to reconstruct the gene family content in ancestral nodes. With ALE, some larger gene families had to be eliminated due to numerical issues. I assume alerax can handle this now? Could you guide me on how to extract the necessary information from the result files? Thank you very much for your assistance. Best regards, Mia test_set.tar.gz <https://github.com/BenoitMorel/AleRax/files/15157149/test_set.tar.gz> — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UMQ7HHKIIP5J4MEAGTY737ZFAVCNFSM6AAAAABGDH7TOWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGI2TQOBZHE> . You are receiving this because you commented.Message ID: ***@***.***>