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 02:12:34 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/2_msa/Q8NBP7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/3_mltree/Q8NBP7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/4_raxmlng_ancestral/Q8NBP7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675554 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/Q8NBP7/2_msa/Q8NBP7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 692 sites WARNING: Sequences tr_J3KFU8_J3KFU8_COCIM_246410 and tr_A0A0J6YFG8_A0A0J6YFG8_COCIT_404692 are exactly identical! WARNING: Sequences tr_J3KJ41_J3KJ41_COCIM_246410 and tr_A0A0J6Y3Y3_A0A0J6Y3Y3_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VY68_B2VY68_PYRTR_426418 and tr_A0A2W1I4R7_A0A2W1I4R7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2K6H237_A0A2K6H237_PANTR_9598 and sp_A8T644_PCSK9_PANTR_9598 are exactly identical! WARNING: Sequences tr_F9FGE3_F9FGE3_FUSOF_660025 and tr_A0A0D2XQ22_A0A0D2XQ22_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FGE3_F9FGE3_FUSOF_660025 and tr_N4ULL5_N4ULL5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FGE3_F9FGE3_FUSOF_660025 and tr_X0CTH6_X0CTH6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FGE3_F9FGE3_FUSOF_660025 and tr_A0A2H3TA24_A0A2H3TA24_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FP14_F9FP14_FUSOF_660025 and tr_N4UNF7_N4UNF7_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FP14_F9FP14_FUSOF_660025 and tr_X0BLE8_X0BLE8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FP14_F9FP14_FUSOF_660025 and tr_A0A2H3T088_A0A2H3T088_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9F7K8_E9F7K8_METRA_655844 and tr_A0A0D9PC39_A0A0D9PC39_METAN_1291518 are exactly identical! WARNING: Sequences tr_A2QMZ7_A2QMZ7_ASPNC_425011 and tr_A0A319AQY0_A0A319AQY0_9EURO_1450533 are exactly identical! WARNING: Sequences tr_W4YIL5_W4YIL5_STRPU_7668 and tr_W4YSR0_W4YSR0_STRPU_7668 are exactly identical! WARNING: Sequences tr_G2YRA6_G2YRA6_BOTF4_999810 and tr_M7TMP3_M7TMP3_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SH33_F2SH33_TRIRC_559305 and tr_A0A178F2K0_A0A178F2K0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2SLX7_F2SLX7_TRIRC_559305 and tr_A0A178EPB0_A0A178EPB0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G7NVZ1_G7NVZ1_MACFA_9541 and sp_A8T662_PCSK9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A015IHP5_A0A015IHP5_9GLOM_1432141 and tr_A0A2H5TKG7_A0A2H5TKG7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015IYZ8_A0A015IYZ8_9GLOM_1432141 and tr_A0A2H5TVT0_A0A2H5TVT0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015J6Y2_A0A015J6Y2_9GLOM_1432141 and tr_A0A2H5RRK9_A0A2H5RRK9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JEA3_A0A015JEA3_9GLOM_1432141 and tr_U9SXU5_U9SXU5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JK52_A0A015JK52_9GLOM_1432141 and tr_A0A2H5UAL6_A0A2H5UAL6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JKS3_A0A015JKS3_9GLOM_1432141 and tr_U9TKF5_U9TKF5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015K2K4_A0A015K2K4_9GLOM_1432141 and tr_A0A2H5TNC2_A0A2H5TNC2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015KMD2_A0A015KMD2_9GLOM_1432141 and tr_U9UV35_U9UV35_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015LET1_A0A015LET1_9GLOM_1432141 and tr_A0A2H5TMX3_A0A2H5TMX3_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094DUL0_A0A094DUL0_9PEZI_1420912 and tr_A0A1B8GS00_A0A1B8GS00_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A1NFZ2_A0A0A1NFZ2_9FUNG_58291 and tr_A0A367IWY4_A0A367IWY4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1PAB7_A0A0A1PAB7_9FUNG_58291 and tr_A0A367JWE3_A0A367JWE3_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A100IE06_A0A100IE06_ASPNG_5061 and tr_A0A1L9MXZ2_A0A1L9MXZ2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1C3YLW9_A0A1C3YLW9_GIBZE_229533 and tr_A0A2T4GDL6_A0A2T4GDL6_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1S3JBM4_A0A1S3JBM4_LINUN_7574 and tr_A0A1S3KAC7_A0A1S3KAC7_LINUN_7574 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.raxml.reduced.phy Alignment comprises 1 partitions and 692 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 692 Gaps: 45.01 % Invariant sites: 0.14 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.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/Q8NBP7/3_mltree/Q8NBP7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 173 / 13840 [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: -332968.306028 [00:00:00 -332968.306028] Initial branch length optimization [00:00:01 -331952.248820] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -330695.062604 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.121427,0.257977) (0.131482,0.329954) (0.338321,0.834922) (0.408770,1.572571) 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/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBP7/4_raxmlng_ancestral/Q8NBP7.raxml.log Analysis started: 03-Jun-2021 02:12:34 / finished: 03-Jun-2021 02:13:34 Elapsed time: 59.868 seconds Consumed energy: 4.270 Wh