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Emmanuel Cantú
Mar 14, 2019, 3:33:15 PM3/14/19
to IQ-TREE
I tried to do a mixed analysis of morphological data and DNA with this line of comand
iqtree -sp partition_file.nex -pre result_morf_mol -bb 1000 -bnni -alrt 1000 -nt AUTO -o Gmelina_arborea_KR532195_1_isolate_G135
I think it was caused by the -bnni command, here are the first 10 lines and last 10 of the log file:
IQ-TREE multicore version 1.6.10 for Windows 64-bit built Feb 19 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: LAPTOP-6P500TSE (AVX2, FMA3, 7 GB RAM)
Command: iqtree -sp partition_file.nex -pre result_morf_mol -bb 1000 -bspec GENE -alrt 1000 -nt AUTO -o Gmelina_arborea_KR532195_1_isolate_G135
Seed: 855323 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 14 13:08:33 2019
Kernel: AVX+FMA - auto-detect threads (4 CPU cores detected)
Iteration 250 / LogL: -20797.671 / Time: 0h:8m:36s (0h:0m:47s left)
Iteration 260 / LogL: -20789.669 / Time: 0h:8m:53s (0h:0m:26s left)
Iteration 270 / LogL: -20778.250 / Time: 0h:9m:8s (0h:0m:6s left)
Refining ufboot trees with NNI 1 branch...
(((1:0.3896749368,(((((((((((((10:0.0325456956,11:0.0168967483):0.0320648571,(23:0.1279991260,129:0.0000029038):0.0000029038):0.0158507170,88:0.0000026713):0.0749075180,((((18:0.0962550812,150:0.0000029038):0.0000024316,90:0.1256861279):0.0000023126,(100:0.0000025881,143:0.0000026611):0.0994549789):0.0000022551,(((102:0.0000021999,104:0.0000021999):0.0000021999,103:0.0000021999):0.0000024828,101:0.0000024828):0.0000028817):0.1068783450):0.0000021286,116:0.1130224046):0.0000020127,(((21:0.2012130542,((37:0.0462840271,(114:0.0000021999,(((52:0.0000024302,54:0.0000021999):0.0000024302,53:0.0000021999):0.1287720466,82:0.4152329879):0.0177654091):0.0481579224):0.2663006184,59:0.0469042496):0.0000020649):0.0000029038,125:0.3131179630):0.0000029038,76:9.9999980523):0.0000029222):0.0289279319,((((30:0.0437326524,121:0.0340951738):0.1360001585,31:0.0000022174):0.0863378402,((78:0.0000027878,(106:0.0935373817,123:0.0000027204):0.0875908949):0.0000021825,((62:0.0652024604,134:0.0317689746):0.0289998625,117:0.0317132625):0.0145218092):0.0000027204):0.0000023849,91:0.0848185285):0.0000028141):0.0000026388,((((4:0.0000029038,154:0.0000029038):0.1086833274,95:0.0709743548):0.0336918278,35:0.2202508388):0.0000027410,((((((((83:0.0000029038,137:0.0000029038):0.0000029038,145:0.0318507223):0.0000028501,24:0.0671496062):0.1163632117,113:0.0000021856):0.0493687020,120:0.0891022994):0.0000029038,((77:0.9521748729,156:0.0000029038):0.1299934598,87:0.0683799915):0.0666688262):0.0000029038,132:0.0719871003):0.0000029038,(43:0.1792595960,(70:0.1792595687,(71:0.0000029038,72:0.0000029038):0.0000029038):0.0591965195):0.0000029038):0.0000029038):0.0000026388):0.1919439432,(((((74:0.2397350603,141:0.0000021606):0.0000021606,144:0.0000021606):0.0000021606,((128:0.2850040162,160:0.1401881000):0.0000020578,158:0.0000021606):0.0000021606):0.0000025737,(((33:0.0000027204,34:0.0000029038):0.3088311797,(((42:0.0000021606,(126:0.4203196949,149:0.0000021999):0.1331358842):0.0000020278,140:0.0000021606):0.0000021528,142:0.1354323402):0.0000027828):0.0000028003,(157:0.0877999635,(((((((17:0.0840941514,99:0.1029654368):0.0000025737,135:0.1353901807):0.0000025737,159:0.1027593844):0.0000025737,(47:0.1548360280,94:0.1774610234):0.0875685409):0.0000025737,(56:0.0000027205,57:0.0000021606):0.0000024787):0.1029459857,22:0.0000021606):0.0000020058,((15:0.3704920552,25:0.0074586990):0.1493214917,51:0.0515624746):0.0000023224):0.0000029653):0.0000027376):0.0000025737):0.0904670587,155:0.0000021606):0.0000028811):0.0000027204,((((((((60:0.1835461666,(29:0.1295698642,(14:0.0904633001,(55:0.1791711431,131:0.1690718168):0.0780338092):0.1212762065):0.0000024256):0.0000029038,153:0.1511700112):0.0000029038,20:0.0000029038):0.2280372263,(46:0.0000024255,67:0.1296469338):0.0071269450):0.0261497243,(96:0.1335154030,((86:0.1542942248,136:0.0398665817):0.0608506947,(98:0.0776401471,(39:0.4480576373,((58:0.1386432880,68:0.1982884708):0.4044860131,81:0.0000026679):0.0744850986):0.0264702527):0.0000028638):0.0602071661):0.0655664717):0.0292291228,50:0.1567111055):0.0000029038,((26:0.1401885999,(36:0.1309895011,115:0.1931695740):0.0000029038):0.0000029038,49:0.3105617502):0.0000022923):0.0000026316,((93:0.0000029038,((44:0.1781618662,124:0.0639473086):0.0639395247,48:0.4450674986):0.0000028838):0.0000029038,(79:0.0000029038,80:0.0000029038):0.3412277486):0.0000029038):0.0290866522):0.0922166898,((((((8:0.0000023621,45:0.0921891125):0.1780212807,((((((((9:0.0000021999,130:0.2186368847):0.0000021999,(112:0.0000027051,151:0.1792594954):0.0000027051):0.0000027051,(108:0.0841047554,(12:0.2633638104,107:0.4663465328):0.0000020260):0.0000028933):0.0000027051,146:0.0000021999):0.0000027051,((19:0.0000021999,97:0.0000021999):0.2703979651,(((38:0.0325606850,((84:0.0000021999,85:0.0000021999):0.1104554018,147:0.0000021999):0.1049083939):0.0697704195,89:0.0734057017):0.0682403653,(111:0.0807081810,(110:0.0393773803,109:0.0000021999):0.0000021999):0.0807091926):0.0000027436):0.0000027436):0.0310322332,139:0.0746768415):0.0000028078,64:0.1631864642):0.0000028078,138:0.0807081891):0.0000021606):0.0000021606,133:0.0775753556):0.0000029361,((28:0.0236726393,66:0.2972577802):0.2558968123,(((27:0.0000021999,69:0.1115417063):0.0726950110,65:0.0746767041):0.0000021999,105:0.0000021999):0.0000021999):0.0902744482):0.0000026905,((((16:0.0816303798,122:0.0000021999):0.1718684432,(((73:0.2162610731,118:0.0000025881):0.0000023940,119:0.0000029038):0.0000026388,152:0.1146833249):0.0000029653):0.0000022926,(40:0.1776610824,61:0.3840130918):0.0000021560):0.0000025982,63:0.1354314619):0.0000021219):0.0298033131,127:0.0000021606):0.0606337244):0.0000026657,((13:0.1700924289,(41:0.1882074045,92:0.1581603250):0.0710764296):0.0000027436,((((5:0.0000021999,7:0.0000021999):0.0000021999,6:0.0000021999):0.1175170815,148:0.0906328035):0.0358464762,(32:0.4422233208,75:0.0918389165):0.0000027436):0.0000029361):0.0000029361):0.2207213131,161:0.3172464783):0.0000026749):0.0000029038,2:0.0351838623):0.2224078273,3:0.5857666480,0:0.0799459838);
ERROR: phylokernelnew.h:3179: double PhyloTree::computeLikelihoodFromBufferGenericSIMD() [VectorClass = Vec4d, FMA = true, SITE_MODEL = false]: Assertion `prob_const < 1.0 && prob_const >= 0.0' failed.
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: result_morf_mol.log
ERROR: *** Alignment files (if possible)
IQ-TREE multicore version 1.6.10 for Windows 64-bit built Feb 19 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: LAPTOP-6P500TSE (AVX2, FMA3, 7 GB RAM)
Command: iqtree -sp partition_file.nex -pre result_morf_mol -bb 1000 -bspec GENE -alrt 1000 -nt AUTO -o Gmelina_arborea_KR532195_1_isolate_G135
Seed: 855323 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 14 13:08:33 2019
Kernel: AVX+FMA - auto-detect threads (4 CPU cores detected)
Iteration 250 / LogL: -20797.671 / Time: 0h:8m:36s (0h:0m:47s left)
Iteration 260 / LogL: -20789.669 / Time: 0h:8m:53s (0h:0m:26s left)
Iteration 270 / LogL: -20778.250 / Time: 0h:9m:8s (0h:0m:6s left)
Refining ufboot trees with NNI 1 branch...
(((1:0.3896749368,(((((((((((((10:0.0325456956,11:0.0168967483):0.0320648571,(23:0.1279991260,129:0.0000029038):0.0000029038):0.0158507170,88:0.0000026713):0.0749075180,((((18:0.0962550812,150:0.0000029038):0.0000024316,90:0.1256861279):0.0000023126,(100:0.0000025881,143:0.0000026611):0.0994549789):0.0000022551,(((102:0.0000021999,104:0.0000021999):0.0000021999,103:0.0000021999):0.0000024828,101:0.0000024828):0.0000028817):0.1068783450):0.0000021286,116:0.1130224046):0.0000020127,(((21:0.2012130542,((37:0.0462840271,(114:0.0000021999,(((52:0.0000024302,54:0.0000021999):0.0000024302,53:0.0000021999):0.1287720466,82:0.4152329879):0.0177654091):0.0481579224):0.2663006184,59:0.0469042496):0.0000020649):0.0000029038,125:0.3131179630):0.0000029038,76:9.9999980523):0.0000029222):0.0289279319,((((30:0.0437326524,121:0.0340951738):0.1360001585,31:0.0000022174):0.0863378402,((78:0.0000027878,(106:0.0935373817,123:0.0000027204):0.0875908949):0.0000021825,((62:0.0652024604,134:0.0317689746):0.0289998625,117:0.0317132625):0.0145218092):0.0000027204):0.0000023849,91:0.0848185285):0.0000028141):0.0000026388,((((4:0.0000029038,154:0.0000029038):0.1086833274,95:0.0709743548):0.0336918278,35:0.2202508388):0.0000027410,((((((((83:0.0000029038,137:0.0000029038):0.0000029038,145:0.0318507223):0.0000028501,24:0.0671496062):0.1163632117,113:0.0000021856):0.0493687020,120:0.0891022994):0.0000029038,((77:0.9521748729,156:0.0000029038):0.1299934598,87:0.0683799915):0.0666688262):0.0000029038,132:0.0719871003):0.0000029038,(43:0.1792595960,(70:0.1792595687,(71:0.0000029038,72:0.0000029038):0.0000029038):0.0591965195):0.0000029038):0.0000029038):0.0000026388):0.1919439432,(((((74:0.2397350603,141:0.0000021606):0.0000021606,144:0.0000021606):0.0000021606,((128:0.2850040162,160:0.1401881000):0.0000020578,158:0.0000021606):0.0000021606):0.0000025737,(((33:0.0000027204,34:0.0000029038):0.3088311797,(((42:0.0000021606,(126:0.4203196949,149:0.0000021999):0.1331358842):0.0000020278,140:0.0000021606):0.0000021528,142:0.1354323402):0.0000027828):0.0000028003,(157:0.0877999635,(((((((17:0.0840941514,99:0.1029654368):0.0000025737,135:0.1353901807):0.0000025737,159:0.1027593844):0.0000025737,(47:0.1548360280,94:0.1774610234):0.0875685409):0.0000025737,(56:0.0000027205,57:0.0000021606):0.0000024787):0.1029459857,22:0.0000021606):0.0000020058,((15:0.3704920552,25:0.0074586990):0.1493214917,51:0.0515624746):0.0000023224):0.0000029653):0.0000027376):0.0000025737):0.0904670587,155:0.0000021606):0.0000028811):0.0000027204,((((((((60:0.1835461666,(29:0.1295698642,(14:0.0904633001,(55:0.1791711431,131:0.1690718168):0.0780338092):0.1212762065):0.0000024256):0.0000029038,153:0.1511700112):0.0000029038,20:0.0000029038):0.2280372263,(46:0.0000024255,67:0.1296469338):0.0071269450):0.0261497243,(96:0.1335154030,((86:0.1542942248,136:0.0398665817):0.0608506947,(98:0.0776401471,(39:0.4480576373,((58:0.1386432880,68:0.1982884708):0.4044860131,81:0.0000026679):0.0744850986):0.0264702527):0.0000028638):0.0602071661):0.0655664717):0.0292291228,50:0.1567111055):0.0000029038,((26:0.1401885999,(36:0.1309895011,115:0.1931695740):0.0000029038):0.0000029038,49:0.3105617502):0.0000022923):0.0000026316,((93:0.0000029038,((44:0.1781618662,124:0.0639473086):0.0639395247,48:0.4450674986):0.0000028838):0.0000029038,(79:0.0000029038,80:0.0000029038):0.3412277486):0.0000029038):0.0290866522):0.0922166898,((((((8:0.0000023621,45:0.0921891125):0.1780212807,((((((((9:0.0000021999,130:0.2186368847):0.0000021999,(112:0.0000027051,151:0.1792594954):0.0000027051):0.0000027051,(108:0.0841047554,(12:0.2633638104,107:0.4663465328):0.0000020260):0.0000028933):0.0000027051,146:0.0000021999):0.0000027051,((19:0.0000021999,97:0.0000021999):0.2703979651,(((38:0.0325606850,((84:0.0000021999,85:0.0000021999):0.1104554018,147:0.0000021999):0.1049083939):0.0697704195,89:0.0734057017):0.0682403653,(111:0.0807081810,(110:0.0393773803,109:0.0000021999):0.0000021999):0.0807091926):0.0000027436):0.0000027436):0.0310322332,139:0.0746768415):0.0000028078,64:0.1631864642):0.0000028078,138:0.0807081891):0.0000021606):0.0000021606,133:0.0775753556):0.0000029361,((28:0.0236726393,66:0.2972577802):0.2558968123,(((27:0.0000021999,69:0.1115417063):0.0726950110,65:0.0746767041):0.0000021999,105:0.0000021999):0.0000021999):0.0902744482):0.0000026905,((((16:0.0816303798,122:0.0000021999):0.1718684432,(((73:0.2162610731,118:0.0000025881):0.0000023940,119:0.0000029038):0.0000026388,152:0.1146833249):0.0000029653):0.0000022926,(40:0.1776610824,61:0.3840130918):0.0000021560):0.0000025982,63:0.1354314619):0.0000021219):0.0298033131,127:0.0000021606):0.0606337244):0.0000026657,((13:0.1700924289,(41:0.1882074045,92:0.1581603250):0.0710764296):0.0000027436,((((5:0.0000021999,7:0.0000021999):0.0000021999,6:0.0000021999):0.1175170815,148:0.0906328035):0.0358464762,(32:0.4422233208,75:0.0918389165):0.0000027436):0.0000029361):0.0000029361):0.2207213131,161:0.3172464783):0.0000026749):0.0000029038,2:0.0351838623):0.2224078273,3:0.5857666480,0:0.0799459838);
ERROR: phylokernelnew.h:3179: double PhyloTree::computeLikelihoodFromBufferGenericSIMD() [VectorClass = Vec4d, FMA = true, SITE_MODEL = false]: Assertion `prob_const < 1.0 && prob_const >= 0.0' failed.
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: result_morf_mol.log
ERROR: *** Alignment files (if possible)
One friend suggest me to change the -bnni command for the -bspec GENE command, but i want to make sure that was the problem.
Thanks.
Minh Bui
Mar 17, 2019, 8:27:08 PM3/17/19
to IQ-TREE, Emmanuel Cantú, Hoang Thi Diep
Hi Emmanuel, CC Diep,
It looks like -bnni option does not work with GENE resampling (-bspec GENE)… We’ll take a note, but for now please avoid doing these two options together.
Thanks!
Minh
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