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 03-Jun-2021 01:57:52 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/2_msa/P30613_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/3_mltree/P30613.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/4_raxmlng_ancestral/P30613 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674672 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/P30613/2_msa/P30613_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 574 sites WARNING: Sequences tr_B4Q8K9_B4Q8K9_DROSI_7240 and tr_B4I2Q7_B4I2Q7_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I2ZNS9_A0A2I2ZNS9_GORGO_9595 and tr_A0A2I3TKQ7_A0A2I3TKQ7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZNS9_A0A2I2ZNS9_GORGO_9595 and tr_A0A2R9C711_A0A2R9C711_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q7RVA8_KPYK_NEUCR_367110 and tr_G4UVY3_G4UVY3_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q29KF0_Q29KF0_DROPS_46245 and tr_B4HBY3_B4HBY3_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8MWA0_B8MWA0_ASPFN_332952 and tr_Q2UPQ1_Q2UPQ1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MWA0_B8MWA0_ASPFN_332952 and tr_Q9HGY6_Q9HGY6_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H9KUV5_H9KUV5_CANLF_9615 and sp_Q29536_KPYR_CANLF_9615 are exactly identical! WARNING: Sequences tr_F9F670_F9F670_FUSOF_660025 and tr_N4U1T5_N4U1T5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9F670_F9F670_FUSOF_660025 and tr_X0CZK6_X0CZK6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9F670_F9F670_FUSOF_660025 and tr_A0A2H3TQF2_A0A2H3TQF2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9F670_F9F670_FUSOF_660025 and tr_A0A2H3H3B2_A0A2H3H3B2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9DCC8_E9DCC8_COCPS_443226 and tr_A0A0J6YH66_A0A0J6YH66_COCIT_404692 are exactly identical! WARNING: Sequences tr_E9F3U0_E9F3U0_METRA_655844 and tr_A0A0D9NX12_A0A0D9NX12_METAN_1291518 are exactly identical! WARNING: Sequences tr_A2QPC7_A2QPC7_ASPNC_425011 and tr_G3XZI6_G3XZI6_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QPC7_A2QPC7_ASPNC_425011 and tr_A0A319A2R6_A0A319A2R6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XEC4_G7XEC4_ASPKW_1033177 and tr_A0A146F1W1_A0A146F1W1_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F9X8R8_F9X8R8_ZYMTI_336722 and tr_A0A0F4H1D6_A0A0F4H1D6_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9X8R8_F9X8R8_ZYMTI_336722 and tr_A0A1X7RQ77_A0A1X7RQ77_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2PY83_F2PY83_TRIEC_559882 and tr_A0A059J2C9_A0A059J2C9_9EURO_1215338 are exactly identical! WARNING: Sequences tr_A0A015KGF1_A0A015KGF1_9GLOM_1432141 and tr_U9SI46_U9SI46_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2I3MSK7_A0A2I3MSK7_PAPAN_9555 and tr_A0A2K6A6L0_A0A2K6A6L0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094ESB3_A0A094ESB3_9PEZI_1420912 and tr_A0A1B8GRW6_A0A1B8GRW6_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8V4A1_A0A0F8V4A1_9EURO_308745 and tr_A0A2T5LWZ0_A0A2T5LWZ0_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V0X9S9_A0A0V0X9S9_9BILA_92179 and tr_A0A0V0VNG3_A0A0V0VNG3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0X9S9_A0A0V0X9S9_9BILA_92179 and tr_A0A0V1LGU7_A0A0V1LGU7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X9S9_A0A0V0X9S9_9BILA_92179 and tr_A0A0V1NP57_A0A0V1NP57_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0X9S9_A0A0V0X9S9_9BILA_92179 and tr_A0A0V0TTS6_A0A0V0TTS6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1LDP2_A0A0V1LDP2_9BILA_6335 and tr_A0A0V1P4Y2_A0A0V1P4Y2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1LDP2_A0A0V1LDP2_9BILA_6335 and tr_A0A0V0TWJ5_A0A0V0TWJ5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100ICT0_A0A100ICT0_ASPNG_5061 and tr_A0A1L9MZ71_A0A1L9MZ71_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A164XN97_A0A164XN97_9HOMO_1314777 and tr_A0A166J9V0_A0A166J9V0_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1V8UES4_A0A1V8UES4_9PEZI_1974281 and tr_A0A1V8TAT9_A0A1V8TAT9_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A319BXZ3_A0A319BXZ3_9EURO_1448315 and tr_A0A2V5I3T1_A0A2V5I3T1_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319BXZ3_A0A319BXZ3_9EURO_1448315 and tr_A0A2V5GTF4_A0A2V5GTF4_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 35 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/P30613/4_raxmlng_ancestral/P30613.raxml.reduced.phy Alignment comprises 1 partitions and 574 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 574 Gaps: 11.49 % Invariant sites: 1.05 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/4_raxmlng_ancestral/P30613.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/P30613/3_mltree/P30613.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 144 / 11520 [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: -189025.913832 [00:00:00 -189025.913832] Initial branch length optimization [00:00:01 -188414.485498] Model parameter optimization (eps = 0.100000) [00:00:36] Tree #1, final logLikelihood: -187909.326962 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.257780,0.283951) (0.281521,0.439007) (0.213175,1.013805) (0.247524,2.371871) 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/P30613/4_raxmlng_ancestral/P30613.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/4_raxmlng_ancestral/P30613.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/4_raxmlng_ancestral/P30613.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30613/4_raxmlng_ancestral/P30613.raxml.log Analysis started: 03-Jun-2021 01:57:52 / finished: 03-Jun-2021 01:58:34 Elapsed time: 41.639 seconds Consumed energy: 2.840 Wh