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 12-Jul-2021 18:03:29 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/2_msa/P0C7U3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/3_mltree/P0C7U3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102209 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/300621_run/phylogeny-snakemake/results/P0C7U3/2_msa/P0C7U3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 371 sites WARNING: Sequences sp_Q5Y5T5_ZDHC8_MOUSE_10090 and tr_Q2THW6_Q2THW6_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I3HZQ0_A0A2I3HZQ0_NOMLE_61853 and tr_A0A2I3LXQ9_A0A2I3LXQ9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HZQ0_A0A2I3HZQ0_NOMLE_61853 and tr_A0A0D9RIB1_A0A0D9RIB1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HZQ0_A0A2I3HZQ0_NOMLE_61853 and tr_A0A2K6B672_A0A2K6B672_MACNE_9545 are exactly identical! WARNING: Sequences tr_B2W9G8_B2W9G8_PYRTR_426418 and tr_A0A2W1G475_A0A2W1G475_9PLEO_45151 are exactly identical! WARNING: Sequences tr_H2P3N7_H2P3N7_PONAB_9601 and tr_A0A1U7TW36_A0A1U7TW36_TARSY_1868482 are exactly identical! WARNING: Sequences tr_Q29NW1_Q29NW1_DROPS_46245 and tr_B4GJP3_B4GJP3_DROPE_7234 are exactly identical! WARNING: Sequences tr_K7DNY2_K7DNY2_PANTR_9598 and sp_Q9ULC8_ZDHC8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A158NV05_A0A158NV05_ATTCE_12957 and tr_A0A195BVE3_A0A195BVE3_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0GIS7_A0A0E0GIS7_ORYNI_4536 and tr_A0A0E0NRC7_A0A0E0NRC7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2QVR5_A2QVR5_ASPNC_425011 and tr_A0A319A9M5_A0A319A9M5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XAR9_G7XAR9_ASPKW_1033177 and tr_A0A146F7U1_A0A146F7U1_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2YNB4_A2YNB4_ORYSI_39946 and tr_I1QBW2_I1QBW2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8AQH2_B8AQH2_ORYSI_39946 and tr_Q10Q54_Q10Q54_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8BEL1_B8BEL1_ORYSI_39946 and tr_A0A0E0B6M9_A0A0E0B6M9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B8BEL1_B8BEL1_ORYSI_39946 and tr_A0A0P0XQE0_A0A0P0XQE0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QKB9_I1QKB9_ORYGL_4538 and tr_Q6ZJ22_Q6ZJ22_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QTI5_I1QTI5_ORYGL_4538 and tr_A0A0D3HCF1_A0A0D3HCF1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G3SP05_G3SP05_LOXAF_9785 and tr_A0A2Y9EAG5_A0A2Y9EAG5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A0E0CX06_A0A0E0CX06_9ORYZ_40149 and tr_A0A0D9Z3R0_A0A0D9Z3R0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0NAU6_A0A0E0NAU6_ORYRU_4529 and tr_A0A0D3F1N0_A0A0D3F1N0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_M4D1Y6_M4D1Y6_BRARP_51351 and tr_A0A078GJR0_A0A078GJR0_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A015M2I8_A0A015M2I8_9GLOM_1432141 and tr_A0A2H5UI46_A0A2H5UI46_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067DZX1_A0A067DZX1_CITSI_2711 and tr_A0A2H5Q291_A0A2H5Q291_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067FMF0_A0A067FMF0_CITSI_2711 and tr_V4SQN2_V4SQN2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078F841_A0A078F841_BRANA_3708 and tr_A0A0D3BAE6_A0A0D3BAE6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078HQN2_A0A078HQN2_BRANA_3708 and tr_A0A0D3CZ84_A0A0D3CZ84_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2RH98_A0A0D2RH98_GOSRA_29730 and tr_A0A1U8JZL8_A0A1U8JZL8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A151J553_A0A151J553_9HYME_471704 and tr_A0A195F742_A0A195F742_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3XQB4_A0A1S3XQB4_TOBAC_4097 and tr_A0A1U7WMI6_A0A1U7WMI6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YUD2_A0A1S3YUD2_TOBAC_4097 and tr_A0A1U7V958_A0A1U7V958_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4A9Y5_A0A1S4A9Y5_TOBAC_4097 and tr_A0A1U7VJX1_A0A1U7VJX1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DGB3_A0A1S4DGB3_TOBAC_4097 and tr_A0A1U7X2B0_A0A1U7X2B0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DRH6_A0A1S4DRH6_TOBAC_4097 and tr_A0A1J6HW95_A0A1J6HW95_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1U8GRR7_A0A1U8GRR7_CAPAN_4072 and tr_A0A2G3CIX0_A0A2G3CIX0_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G2YD95_A0A2G2YD95_CAPAN_4072 and tr_A0A2G3B7F3_A0A2G3B7F3_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5MP14_A0A2K5MP14_CERAT_9531 and tr_A0A2K5ZMM8_A0A2K5ZMM8_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 37 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.raxml.reduced.phy Alignment comprises 1 partitions and 371 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 371 Gaps: 35.65 % Invariant sites: 1.08 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.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/300621_run/phylogeny-snakemake/results/P0C7U3/3_mltree/P0C7U3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 93 / 7440 [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: -169974.489637 [00:00:00 -169974.489637] Initial branch length optimization [00:00:01 -164013.039181] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -163299.914791 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.081146,0.157790) (0.172935,0.931558) (0.360626,0.610601) (0.385293,1.572565) 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/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P0C7U3/4_raxmlng_ancestral/P0C7U3.raxml.log Analysis started: 12-Jul-2021 18:03:29 / finished: 12-Jul-2021 18:04:18 Elapsed time: 49.432 seconds Consumed energy: 4.542 Wh