RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 02:14:56 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/2_msa/Q14683_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/3_mltree/Q14683.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675696 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/2_msa/Q14683_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1233 sites WARNING: Sequences sp_Q9CU62_SMC1A_MOUSE_10090 and tr_I3M666_I3M666_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q9CU62_SMC1A_MOUSE_10090 and tr_A0A1U7R271_A0A1U7R271_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_E2QV07_E2QV07_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_D2HVV0_D2HVV0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_M3WJP4_M3WJP4_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_A0A2U3WEH7_A0A2U3WEH7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_A0A2U3XEV5_A0A2U3XEV5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_A0A2Y9E8X5_A0A2Y9E8X5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YEA2_M3YEA2_MUSPF_9669 and tr_A0A2Y9IH34_A0A2Y9IH34_ENHLU_391180 are exactly identical! WARNING: Sequences tr_J3K3R4_J3K3R4_COCIM_246410 and tr_A0A0J6YGE2_A0A0J6YGE2_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QVZ6_B6QVZ6_TALMQ_441960 and tr_A0A093VBM7_A0A093VBM7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_H2R1Q9_H2R1Q9_PANTR_9598 and tr_A0A2R8ZJD2_A0A2R8ZJD2_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and sp_Q14683_SMC1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_G7NRH2_G7NRH2_MACMU_9544 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_F7IDJ8_F7IDJ8_CALJA_9483 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_G7Q2S9_G7Q2S9_MACFA_9541 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_A0A2K5N0E4_A0A2K5N0E4_CERAT_9531 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_A0A2K6BEL4_A0A2K6BEL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_A0A2K5ZAB2_A0A2K5ZAB2_MANLE_9568 are exactly identical! WARNING: Sequences tr_K7CY55_K7CY55_PANTR_9598 and tr_A0A2R9CBK0_A0A2R9CBK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_E9EUG4_E9EUG4_METRA_655844 and tr_A0A0D9NND8_A0A0D9NND8_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A087ZYL5_A0A087ZYL5_APIME_7460 and tr_A0A2A3EF39_A0A2A3EF39_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0JCY0_A0A0E0JCY0_ORYNI_4536 and tr_A0A0E0RKM3_A0A0E0RKM3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_G7XC59_G7XC59_ASPKW_1033177 and tr_A0A100IUA4_A0A100IUA4_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XC59_G7XC59_ASPKW_1033177 and tr_A0A1L9N8K6_A0A1L9N8K6_ASPTU_767770 are exactly identical! WARNING: Sequences sp_O97593_SMC1A_BOVIN_9913 and tr_A0A1S3A8C6_A0A1S3A8C6_ERIEU_9365 are exactly identical! WARNING: Sequences sp_O97593_SMC1A_BOVIN_9913 and tr_A0A2Y9FH67_A0A2Y9FH67_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A015ISC1_A0A015ISC1_9GLOM_1432141 and tr_A0A2H5SX36_A0A2H5SX36_RHIID_747089 are exactly identical! WARNING: Sequences tr_X0CBN7_X0CBN7_FUSOX_1089458 and tr_A0A2H3SXS8_A0A2H3SXS8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A164XX66_A0A164XX66_9HOMO_1314777 and tr_A0A166AHE3_A0A166AHE3_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A2U4C0Y6_A0A2U4C0Y6_TURTR_9739 and tr_A0A2Y9MSS3_A0A2Y9MSS3_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.reduced.phy Alignment comprises 1 partitions and 1233 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1233 Gaps: 12.39 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/3_mltree/Q14683.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 309 / 24720 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -631616.081461 [00:00:00 -631616.081461] Initial branch length optimization [00:00:03 -630891.374602] Model parameter optimization (eps = 0.100000) [00:00:54] Tree #1, final logLikelihood: -629797.454857 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.169685,0.227460) (0.146523,0.337485) (0.394133,0.870747) (0.289659,1.963564) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14683/4_raxmlng_ancestral/Q14683.raxml.log Analysis started: 03-Jun-2021 02:14:56 / finished: 03-Jun-2021 02:16:01 Elapsed time: 65.303 seconds Consumed energy: 5.163 Wh