carrde
commented
1 year ago I'm having the same error happen when trying to run ModelTest on my data set so would be interested to know the solution.
Open liaochenlanruo opened 3 years ago
carrde
commented
1 year ago I'm having the same error happen when trying to run ModelTest on my data set so would be interested to know the solution.
mmaeke
commented
10 months ago I am currently also running in some troubles running modeltest..
LH mismatch: 0.000000000000 != -2997523.715124555863
modeltest-ng: /opt/conda/conda-bld/modeltest-ng_1646252428554/work/libs/pll-modules/src/algorithm/algo_search.c:1282: pllmod_algo_spr_round: Assertion `fabs(loglh - best_lh) < 1e-6' failed.
Aborted
I have no idea why the error always happens, please help me. The running log is shown below: Physical cores: 72 Logical cores: 144 Memory: 1.01e+03GB Extensions: AVX
WARNING: MSA has not enough sites to infer reliable results Creating new checkpoint file: Roary.modeltest_aa.ckp
ModelTest-NG vx.y.z
Input data: MSA: Roary.core.protein.fasta.gb Tree: Maximum likelihood file: -
taxa: 68
sites: 408785
patterns: 28829
Max. thread mem: 616 MB
Output: Log: Roary.modeltest_aa.log Starting tree: Roary.modeltest_aa.tree Results: Roary.modeltest_aa.out
Selection options:
protein matrices: 19
protein models: 152
include model parameters: Uniform: true p-inv (+I): true gamma (+G): true both (+I+G): true free rates (+R): false fixed freqs: true estimated freqs: false
categories: 4
gamma rates mode: mean asc bias: none epsilon (opt): 0.01 epsilon (par): 0.05 keep branches: false
Additional options: verbosity: very low threads: 25/72 RNG seed: 12345 subtree repeats: enabled
modeltest was called as follows:
Partition 1/1
24/152 WAG+G4+F 3h:55:25 3h:56:00 -2074729.4442 0.0217 - 16/152 STMTREV+I+G4+F 3h:55:29 3h:56:04 -2033708.7978 0.3549 0.8028 7/152 MTREV+I+G4+F 4h:00:55 4h:01:30 -2025846.5708 0.3549 0.8028 19/152 HIVB+I+G4+F 4h:27:24 4h:27:59 -2014905.1744 0.3549 0.8028 25/152 FLU+G4+F 4h:29:57 4h:30:32 -2075228.6745 0.0834 - 2/152 BLOSUM62+I+G4+F5h:10:07 5h:10:42 -2044177.9120 0.3549 0.8028 20/152 PMB+I+G4+F 5h:11:03 5h:11:38 -2042465.2451 0.3549 0.8028 13/152 MTART+I+G4+F 5h:40:35 5h:41:10 -2050105.3186 0.3194 0.8028 22/152 LG+G4+F 5h:52:19 5h:52:54 -2075627.2338 0.0432 - 21/152 HIVB+G4+F 5h:58:39 5h:59:14 -2073488.2801 0.0742 - 3/152 DAYHOFF+I+G4+F 6h:03:26 6h:04:01 -2021315.0281 0.3860 0.8028 18/152 JTT-DCMUT+I+G4+F6h:06:14 6h:06:49 -2009104.3813 0.3549 0.8028 Error: 0.00000 vs -2183213.80553 [0] Error: 0.00000 vs -2183213.80553 [0] Error: 0.00000 vs -2183213.80553 [0] Error: 0.00000 vs -2183213.80553 [0] 5/152 DCMUT+I+G4+F 6h:29:15 6h:29:50 -2021275.3169 0.3859 0.8028 14/152 MTZOA+I+G4+F 6h:39:37 6h:40:12 -2028414.8689 0.3549 0.8028 12/152 MTMAM+I+G4+F 6h:57:11 6h:57:46 -2040743.0044 0.3343 0.8028 10/152 CPREV+I+G4+F 6h:57:33 6h:58:08 -2021137.9856 0.3855 0.8028 8/152 WAG+I+G4+F 6h:58:20 6h:58:55 -2020229.8723 0.3549 0.8028 29/152 DAYHOFF+G4+F 3h:33:31 7h:35:01 -2075187.3374 0.0416 - 28/152 HIVW+G4+F 3h:44:51 7h:40:55 -2097330.8131 0.0596 - 9/152 RTREV+I+G4+F 7h:42:58 7h:43:33 -2028641.9863 0.3549 0.8028 23/152 STMTREV+G4+F 7h:54:14 7h:54:49 -2089505.1153 0.0218 - 4/152 LG+I+G4+F 7h:54:36 7h:55:11 -2020285.1932 0.3549 0.8028 6/152 JTT+I+G4+F 7h:58:19 7h:58:54 -2008845.3845 0.3549 0.8028 30/152 BLOSUM62+G4+F 4h:30:15 8h:58:14 -2099069.7639 0.0216 - 15/152 HIVW+I+G4+F 9h:16:41 9h:17:16 -2037178.7370 0.3549 0.8028 37/152 DCMUT+G4+F 3h:28:25 9h:32:26 -2075370.0225 0.0390 - 27/152 MTREV+G4+F 5h:39:43 9h:35:43 -2081131.5080 0.0974 - 11/152 VT+I+G4+F 9h:37:32 9h:38:07 -2025429.3813 0.3549 0.8028 38/152 MTMAM+G4+F 3h:42:21 9h:49:10 -2103881.5031 0.1016 - 26/152 JTT-DCMUT+G4+F 10h:05:45 10h:06:20 -2062936.2555 0.0218 - 39/152 RTREV+G4+F 3h:40:17 10h:10:07 -2084702.2863 0.0661 - 34/152 MTZOA+G4+F 4h:44:18 10h:25:28 -2086022.5855 0.1004 - 40/152 MTMAM+I+G4 4h:45:54 11h:26:06 -2125255.6269 0.3158 0.8028 46/152 MTREV+I+G4 4h:18:37 12h:02:10 -2108167.8398 0.3549 0.8028 59/152 DAYHOFF+I+F 0h:37:30 12h:03:36 -2059621.0632 - 0.8429 36/152 MTART+G4+F 6h:12:46 12h:12:00 -2112523.1300 0.0997 - 17/152 FLU+I+G4+F 12h:28:09 12h:28:44 -2016934.0297 0.3549 0.8028 31/152 CPREV+G4+F 8h:07:45 12h:38:17 -2075768.5012 0.0674 - 61/152 FLU+I+F 0h:57:00 13h:00:36 -2059859.0709 - 0.8429 49/152 JTT+I+G4 5h:26:34 13h:25:28 -2014946.1124 0.3549 0.8028 60/152 STMTREV+I+F 1h:33:32 13h:35:42 -2073047.0283 - 0.8429 65/152 PMB+I+F 0h:59:45 14h:00:21 -2080242.4891 - 0.8429 45/152 BLOSUM62+I+G4 6h:26:01 14h:06:56 -2051883.3805 0.3549 0.8028 41/152 CPREV+I+G4 7h:10:25 14h:08:11 -2032771.3711 0.3549 0.8028 48/152 MTZOA+I+G4 6h:27:24 14h:22:35 -2095854.7733 0.3371 0.8028 67/152 MTREV+I+F 0h:47:03 14h:22:45 -2067985.4824 - 0.8429 62/152 JTT-DCMUT+I+F 2h:17:42 14h:29:42 -2046852.9698 - 0.8429 56/152 STMTREV+I+G4 4h:39:26 14h:45:46 -2085176.1499 0.3549 0.8028 Error: 0.00000 vs -2186276.29847 [0] Error: 0.00000 vs -2186276.29847 [0] Error: 0.00000 vs -2186276.29847 [0] Error: 0.00000 vs -2186276.29847 [0] Error: 0.00000 vs -2186276.29847 [0] 64/152 HIVB+I+F 2h:12:27 14h:50:44 -2056842.3156 - 0.8429 69/152 RTREV+I+F 0h:54:30 15h:01:26 -2068447.7921 - 0.8429 47/152 MTART+I+G4 7h:09:38 15h:04:27 -2136626.3406 0.3589 0.8429 68/152 WAG+I+F 1h:05:25 15h:05:46 -2058135.6022 - 0.8429 53/152 DCMUT+I+G4 5h:30:33 15h:06:16 -2039527.2935 0.3943 0.8028 63/152 HIVW+I+F 2h:37:34 15h:06:18 -2080228.1968 - 0.8429 35/152 JTT+G4+F 9h:23:57 15h:16:51 -2062600.1435 0.0218 - 52/152 HIVW+I+G4 5h:49:07 15h:21:33 -2094483.4966 0.3549 0.8028 42/152 RTREV+I+G4 8h:29:09 15h:27:17 -2050096.1738 0.3549 0.8028 73/152 BLOSUM62+I+F 0h:58:25 15h:28:07 -2082109.8056 - 0.8429 66/152 VT+I+F 2h:15:55 15h:41:23 -2062398.3179 - 0.8429 74/152 MTMAM+I+F 0h:57:46 15h:43:32 -2097342.1863 - 0.8429 72/152 DCMUT+I+F 1h:34:53 15h:57:38 -2059278.5032 - 0.8429 77/152 MTZOA+I+F 1h:02:14 16h:06:41 -2073035.8061 - 0.8429 70/152 CPREV+I+F 2h:09:46 16h:17:57 -2059727.7496 - 0.8429 75/152 MTART+I+F 1h:34:06 16h:24:50 -2103808.3063 - 0.8429 76/152 LG+I+F 1h:30:58 16h:32:24 -2059163.2491 - 0.8429 43/152 VT+I+G4 9h:34:29 16h:33:24 -2031521.6531 0.3549 0.8028 51/152 HIVB+I+G4 7h:19:08 16h:36:24 -2032726.0664 0.3549 0.8028 71/152 JTT+I+F 2h:18:21 16h:40:56 -2046640.0408 - 0.8429 55/152 FLU+I+G4 7h:15:30 17h:04:40 -2051437.7445 0.3549 0.8028 50/152 PMB+I+G4 8h:42:25 17h:40:39 -2050584.5141 0.3549 0.8028 57/152 LG+I+G4 7h:49:27 17h:59:34 -2027135.0768 0.3549 0.8028 97/152 STMTREV+F 0h:20:44 18h:20:18 -2208571.5638 - - 98/152 DAYHOFF+F 0h:14:59 18h:35:17 -2193551.6487 - - 58/152 DAYHOFF+I+G4 8h:10:16 18h:35:44 -2039335.8079 0.3943 0.8028 82/152 FLU+G4 3h:42:24 19h:03:57 -2108720.3159 0.0753 - 44/152 WAG+I+G4 11h:32:18 19h:07:19 -2027842.3988 0.3549 0.8028 100/152 JTT-DCMUT+F 0h:36:57 19h:12:41 -2179852.1666 - - 99/152 FLU+F 0h:41:28 19h:16:45 -2199254.8389 - - 54/152 JTT-DCMUT+I+G4 9h:43:13 19h:21:20 -2015372.3528 0.3549 0.8028 102/152 HIVB+F 0h:24:12 19h:31:31 -2198889.3210 - - modeltest-ng: /opt/conda/conda-bld/modeltest-ng_1572470208140/work/src/model/parameter_branches.cpp:138: virtual double modeltest::ParameterBranches::optimize(modeltest::mt_opt_params_t*, double, double, bool): Assertion `fabs(cur_loglh - loglh) < 1e-6' failed.