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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:33:58 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/2_msa/O43819_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/3_mltree/O43819.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802838 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/2_msa/O43819_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 266 sites WARNING: Sequences tr_Q9VMX4_Q9VMX4_DROME_7227 and tr_B4I196_B4I196_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KA47_J3KA47_COCIM_246410 and tr_E9DGA6_E9DGA6_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KA47_J3KA47_COCIM_246410 and tr_A0A0J6Y1D5_A0A0J6Y1D5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WBY0_B2WBY0_PYRTR_426418 and tr_A0A2W1GN78_A0A2W1GN78_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3R0Z5_G3R0Z5_GORGO_9595 and tr_K7C047_K7C047_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R0Z5_G3R0Z5_GORGO_9595 and tr_A0A2R9BD90_A0A2R9BD90_PANPA_9597 are exactly identical! WARNING: Sequences tr_C0NWI0_C0NWI0_AJECG_447093 and tr_A6R821_A6R821_AJECN_339724 are exactly identical! WARNING: Sequences tr_Q29L20_Q29L20_DROPS_46245 and tr_B4GSH0_B4GSH0_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QLY2_H2QLY2_PANTR_9598 and tr_A0A2R8ZDD4_A0A2R8ZDD4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_W7MBE9_W7MBE9_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_A0A0D2XQJ2_A0A0D2XQJ2_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_S0DPK7_S0DPK7_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_N4UUU6_N4UUU6_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_A0A2H3TKX6_A0A2H3TKX6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_A0A2H3I2L7_A0A2H3I2L7_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FLB4_F9FLB4_FUSOF_660025 and tr_A0A365N790_A0A365N790_GIBIN_948311 are exactly identical! WARNING: Sequences tr_C6HBT2_C6HBT2_AJECH_544712 and tr_F0UBH6_F0UBH6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4W5R5_J4W5R5_BEAB2_655819 and tr_A0A0A2VLK5_A0A0A2VLK5_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4W5R5_J4W5R5_BEAB2_655819 and tr_A0A2N6NJQ6_A0A2N6NJQ6_BEABA_176275 are exactly identical! WARNING: Sequences tr_A1D7X5_A1D7X5_NEOFI_331117 and tr_A0A0S7DQ45_A0A0S7DQ45_9EURO_293939 are exactly identical! WARNING: Sequences tr_G7XBS5_G7XBS5_ASPKW_1033177 and tr_A0A146FEY7_A0A146FEY7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2X154_A2X154_ORYSI_39946 and tr_A0A0E0NA62_A0A0E0NA62_ORYRU_4529 are exactly identical! WARNING: Sequences tr_F9XPP2_F9XPP2_ZYMTI_336722 and tr_A0A1X7S9E8_A0A1X7S9E8_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_A8WVI9_A8WVI9_CAEBR_6238 and tr_A0A2G5UW45_A0A2G5UW45_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SIQ6_F2SIQ6_TRIRC_559305 and tr_D4B4Y7_D4B4Y7_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SIQ6_F2SIQ6_TRIRC_559305 and tr_A0A059J0F9_A0A059J0F9_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SIQ6_F2SIQ6_TRIRC_559305 and tr_A0A178EZH2_A0A178EZH2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3Y2G3_G3Y2G3_ASPNA_380704 and tr_A0A319AS70_A0A319AS70_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7PTN5_G7PTN5_MACFA_9541 and tr_A0A2K6EBK1_A0A2K6EBK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_L2FWG2_L2FWG2_COLFN_1213859 and tr_T0L9L0_T0L9L0_COLGC_1237896 are exactly identical! WARNING: Sequences tr_W2PTB5_W2PTB5_PHYPN_761204 and tr_A0A0W8BY60_A0A0W8BY60_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A0D3F100_A0A0D3F100_9ORYZ_65489 and tr_A0A0D9YMM0_A0A0D9YMM0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A078ITH1_A0A078ITH1_BRANA_3708 and tr_A0A0D3CLS8_A0A0D3CLS8_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EE41_A0A094EE41_9PEZI_1420912 and tr_A0A1B8GU53_A0A1B8GU53_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D2VY97_A0A0D2VY97_GOSRA_29730 and tr_A0A1U8IWL4_A0A1U8IWL4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F0IKU1_A0A0F0IKU1_ASPPU_1403190 and tr_A0A1S9DI70_A0A1S9DI70_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0A1NTL8_A0A0A1NTL8_9FUNG_58291 and tr_A0A367J8W4_A0A367J8W4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1DEC6_A0A0V1DEC6_TRIBR_45882 and tr_A0A0V1PM87_A0A0V1PM87_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3ZRT3_A0A1S3ZRT3_TOBAC_4097 and tr_A0A1U7V7L4_A0A1U7V7L4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1L9N989_A0A1L9N989_ASPTU_767770 and tr_A0A317V4A7_A0A317V4A7_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1V8U7P4_A0A1V8U7P4_9PEZI_1974281 and tr_A0A1V8SVP7_A0A1V8SVP7_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2H3C460_A0A2H3C460_9AGAR_1076256 and tr_A0A284QUJ3_A0A284QUJ3_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2K5MGX1_A0A2K5MGX1_CERAT_9531 and tr_A0A2K5Y6L5_A0A2K5Y6L5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A319CG26_A0A319CG26_9EURO_1448315 and tr_A0A2V5GQ89_A0A2V5GQ89_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.raxml.reduced.phy Alignment comprises 1 partitions and 266 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 266 Gaps: 17.29 % Invariant sites: 2.26 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/3_mltree/O43819.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 67 / 5360 [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: -129933.841932 [00:00:00 -129933.841932] Initial branch length optimization [00:00:01 -129011.851961] Model parameter optimization (eps = 0.100000) [00:00:30] Tree #1, final logLikelihood: -128839.800736 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120702,0.159631) (0.219413,0.301051) (0.314053,0.869126) (0.345832,1.855600) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43819/4_raxmlng_ancestral/O43819.raxml.log Analysis started: 04-Jun-2021 13:33:58 / finished: 04-Jun-2021 13:34:31 Elapsed time: 33.204 seconds