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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 12-Jul-2021 18:12:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/2_msa/Q3ZCQ8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/3_mltree/Q3ZCQ8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102753 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/Q3ZCQ8/2_msa/Q3ZCQ8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 353 sites WARNING: Sequences tr_J3KDP0_J3KDP0_COCIM_246410 and tr_A0A0J6YCR3_A0A0J6YCR3_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QP66_B6QP66_TALMQ_441960 and tr_A0A093VE15_A0A093VE15_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WKX7_B2WKX7_PYRTR_426418 and tr_A0A2W1H9Q1_A0A2W1H9Q1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NLL7_B8NLL7_ASPFN_332952 and tr_Q2U6G6_Q2U6G6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NLL7_B8NLL7_ASPFN_332952 and tr_A0A1S9D8S5_A0A1S9D8S5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_C6H9P4_C6H9P4_AJECH_544712 and tr_F0UKK5_F0UKK5_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4W3P0_J4W3P0_BEAB2_655819 and tr_A0A0A2WGZ0_A0A0A2WGZ0_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A088AJ70_A0A088AJ70_APIME_7460 and tr_A0A2A3EU14_A0A2A3EU14_APICC_94128 are exactly identical! WARNING: Sequences sp_Q3ZCQ8_TIM50_HUMAN_9606 and tr_A0A2R9CGD7_A0A2R9CGD7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FTH7_A0A0E0FTH7_ORYNI_4536 and tr_A0A0D9YFA9_A0A0D9YFA9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A5AAY9_A5AAY9_ASPNC_425011 and tr_G3XZB1_G3XZB1_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A5AAY9_A5AAY9_ASPNC_425011 and tr_A0A319B2Y5_A0A319B2Y5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XE26_G7XE26_ASPKW_1033177 and tr_A0A146F2C4_A0A146F2C4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XE26_G7XE26_ASPKW_1033177 and tr_A0A317W3W3_A0A317W3W3_9EURO_1448314 are exactly identical! WARNING: Sequences tr_I1PX75_I1PX75_ORYGL_4538 and tr_A0A0D3G9P8_A0A0D3G9P8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0PPW2_A0A0E0PPW2_ORYRU_4529 and tr_Q0DGT4_Q0DGT4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_E3MQW3_E3MQW3_CAERE_31234 and tr_A0A261BW34_A0A261BW34_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3K2P1_E3K2P1_PUCGT_418459 and tr_E3NXP7_E3NXP7_PUCGT_418459 are exactly identical! WARNING: Sequences tr_F2SWA9_F2SWA9_TRIRC_559305 and tr_D4AVT3_D4AVT3_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SWA9_F2SWA9_TRIRC_559305 and tr_A0A178EZE9_A0A178EZE9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2PI65_F2PI65_TRIEC_559882 and tr_A0A059JFU6_A0A059JFU6_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0PCK8_L0PCK8_PNEJ8_1209962 and tr_A0A0W4ZKZ4_A0A0W4ZKZ4_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M4EPV6_M4EPV6_BRARP_51351 and tr_A0A078HYH4_A0A078HYH4_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A015IWV7_A0A015IWV7_9GLOM_1432141 and tr_A0A2I1G768_A0A2I1G768_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A2I3N0U8_A0A2I3N0U8_PAPAN_9555 and tr_A0A2K5LII2_A0A2K5LII2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A078FEN0_A0A078FEN0_BRANA_3708 and tr_A0A0D3BND3_A0A0D3BND3_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094H636_A0A094H636_9PEZI_1420912 and tr_A0A1B8GQ43_A0A1B8GQ43_9PEZI_342668 are exactly identical! WARNING: Sequences tr_X0C0M0_X0C0M0_FUSOX_1089458 and tr_A0A2H3TAN6_A0A2H3TAN6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_V4S6S1_V4S6S1_9ROSI_85681 and tr_A0A2H5N630_A0A2H5N630_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2QR48_A0A0D2QR48_GOSRA_29730 and tr_A0A1U8KMT9_A0A1U8KMT9_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2STY3_A0A0D2STY3_GOSRA_29730 and tr_A0A1U8IYT7_A0A1U8IYT7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2U4Y4_A0A0D2U4Y4_GOSRA_29730 and tr_A0A1U8KVH0_A0A1U8KVH0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F0IRD1_A0A0F0IRD1_ASPPU_1403190 and tr_A0A2G7FRI5_A0A2G7FRI5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8UYM2_A0A0F8UYM2_9EURO_308745 and tr_A0A2T5M938_A0A2T5M938_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1CWW3_A0A0V1CWW3_TRIBR_45882 and tr_A0A0V0VNP7_A0A0V0VNP7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1PGG0_A0A0V1PGG0_9BILA_92180 and tr_A0A0V0TZW3_A0A0V0TZW3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A117NSM1_A0A117NSM1_9EURO_48697 and tr_A0A1V6NQC6_A0A1V6NQC6_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A100ID22_A0A100ID22_ASPNG_5061 and tr_A0A1L9MZ95_A0A1L9MZ95_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A164NZY7_A0A164NZY7_9HOMO_1314777 and tr_A0A165Z1N1_A0A165Z1N1_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4CGG2_A0A1S4CGG2_TOBAC_4097 and tr_A0A1U7VIA5_A0A1U7VIA5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2H3BUZ7_A0A2H3BUZ7_9AGAR_1076256 and tr_A0A284REY2_A0A284REY2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2N5SJA1_A0A2N5SJA1_9BASI_200324 and tr_A0A2N5UW37_A0A2N5UW37_9BASI_200324 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.raxml.reduced.phy Alignment comprises 1 partitions and 353 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 353 Gaps: 19.08 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.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/Q3ZCQ8/3_mltree/Q3ZCQ8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 89 / 7120 [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: -189318.704376 [00:00:00 -189318.704376] Initial branch length optimization [00:00:01 -180577.203902] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -180280.795311 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115982,0.244106) (0.181353,0.341663) (0.383781,0.890932) (0.318883,1.780600) 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/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3ZCQ8/4_raxmlng_ancestral/Q3ZCQ8.raxml.log Analysis started: 12-Jul-2021 18:12:33 / finished: 12-Jul-2021 18:13:04 Elapsed time: 30.574 seconds Consumed energy: 1.774 Wh