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 17-Jul-2021 08:36:47 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/2_msa/Q16740_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626500207 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_300621/phylogeny-snakemake/results/Q16740/2_msa/Q16740_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 277 sites WARNING: Sequences tr_B4Q974_B4Q974_DROSI_7240 and tr_B4HWL9_B4HWL9_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3K3S6_J3K3S6_COCIM_246410 and tr_A0A0J6YB72_A0A0J6YB72_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QVS1_B6QVS1_TALMQ_441960 and tr_A0A093VIU2_A0A093VIU2_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W8W5_B2W8W5_PYRTR_426418 and tr_A0A2W1DEB1_A0A2W1DEB1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q1K659_Q1K659_NEUCR_367110 and tr_G4UH24_G4UH24_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N036_B8N036_ASPFN_332952 and tr_A0A1S9DTW5_A0A1S9DTW5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UEG0_A0A179UEG0_BLAGS_559298 and tr_C5GHD3_C5GHD3_AJEDR_559297 are exactly identical! WARNING: Sequences sp_Q94B60_CLPP4_ARATH_3702 and tr_D7MU32_D7MU32_ARALL_81972 are exactly identical! WARNING: Sequences tr_A0A0E0FM25_A0A0E0FM25_ORYNI_4536 and tr_A0A0E0MX17_A0A0E0MX17_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GA51_A0A0E0GA51_ORYNI_4536 and tr_A0A0E0CNU6_A0A0E0CNU6_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GA51_A0A0E0GA51_ORYNI_4536 and tr_A0A0E0NI67_A0A0E0NI67_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GA51_A0A0E0GA51_ORYNI_4536 and tr_A0A0D9YVD6_A0A0D9YVD6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GA51_A0A0E0GA51_ORYNI_4536 and tr_Q6H7I9_Q6H7I9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A2XVP6_A2XVP6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_I1PN65_I1PN65_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0E0PBR6_A0A0E0PBR6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0D3FY44_A0A0D3FY44_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_Q0JBL5_Q0JBL5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_G3Y1W2_G3Y1W2_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A319BAB1_A0A319BAB1_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XC53_G7XC53_ASPKW_1033177 and tr_A0A146FCV9_A0A146FCV9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XC53_G7XC53_ASPKW_1033177 and tr_A0A1L9N8Y2_A0A1L9N8Y2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XC53_G7XC53_ASPKW_1033177 and tr_A0A317V8A7_A0A317V8A7_9EURO_1448314 are exactly identical! WARNING: Sequences tr_E5SSR0_E5SSR0_TRISP_6334 and tr_A0A0V1CK84_A0A0V1CK84_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SSR0_E5SSR0_TRISP_6334 and tr_A0A0V1A3X4_A0A0V1A3X4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0E0CZJ5_A0A0E0CZJ5_9ORYZ_40149 and tr_A0A0E0NU26_A0A0E0NU26_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0CZJ5_A0A0E0CZJ5_9ORYZ_40149 and tr_A0A0D3FHL4_A0A0D3FHL4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0CZJ5_A0A0E0CZJ5_9ORYZ_40149 and tr_A0A0D9VT80_A0A0D9VT80_9ORYZ_77586 are exactly identical! WARNING: Sequences tr_A0A0E0CZJ5_A0A0E0CZJ5_9ORYZ_40149 and tr_Q50LH5_Q50LH5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2YH10_G2YH10_BOTF4_999810 and tr_M7TDB8_M7TDB8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2T0R1_F2T0R1_TRIRC_559305 and tr_F2PWW6_F2PWW6_TRIEC_559882 are exactly identical! WARNING: Sequences tr_W2Q133_W2Q133_PHYPN_761204 and tr_W2GHV1_W2GHV1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6IPV3_A0A3B6IPV3_WHEAT_4565 and tr_A0A3B6JIS0_A0A3B6JIS0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015IZL8_A0A015IZL8_9GLOM_1432141 and tr_A0A2I1F3C2_A0A2I1F3C2_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A067GSQ1_A0A067GSQ1_CITSI_2711 and tr_V4TB07_V4TB07_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H7P1_A0A067H7P1_CITSI_2711 and tr_V4VWQ3_V4VWQ3_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H7P1_A0A067H7P1_CITSI_2711 and tr_A0A2H5NXJ8_A0A2H5NXJ8_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078GA04_A0A078GA04_BRANA_3708 and tr_A0A0D3EGW9_A0A0D3EGW9_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078HN07_A0A078HN07_BRANA_3708 and tr_A0A0D3D991_A0A0D3D991_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JBU9_A0A078JBU9_BRANA_3708 and tr_A0A0D3DDD7_A0A0D3DDD7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_X0BZT0_X0BZT0_FUSOX_1089458 and tr_A0A2H3SXZ9_A0A2H3SXZ9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_V4TGV0_V4TGV0_9ROSI_85681 and tr_A0A2H5P3M7_A0A2H5P3M7_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2PVC1_A0A0D2PVC1_GOSRA_29730 and tr_A0A1U8N9M7_A0A1U8N9M7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2R6I8_A0A0D2R6I8_GOSRA_29730 and tr_A0A1U8IV12_A0A1U8IV12_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0V0S5L9_A0A0V0S5L9_9BILA_6336 and tr_A0A0V1LHB5_A0A0V1LHB5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S5L9_A0A0V0S5L9_9BILA_6336 and tr_A0A0V0UBR5_A0A0V0UBR5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3X2P4_A0A1S3X2P4_TOBAC_4097 and tr_A0A1J6HXP7_A0A1J6HXP7_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4BBV8_A0A1S4BBV8_TOBAC_4097 and tr_A0A1U7X8P3_A0A1U7X8P3_NICSY_4096 are exactly identical! WARNING: Duplicate sequences found: 48 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.raxml.reduced.phy Alignment comprises 1 partitions and 277 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 277 Gaps: 21.68 % Invariant sites: 2.89 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.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_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 70 / 5600 [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: -105085.972731 [00:00:00 -105085.972731] Initial branch length optimization [00:00:01 -94679.118083] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -93996.347895 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.190166,0.118585) (0.258985,0.215067) (0.231716,0.614388) (0.319133,2.442203) 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_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/4_raxmlng_ancestral/Q16740.raxml.log Analysis started: 17-Jul-2021 08:36:47 / finished: 17-Jul-2021 08:37:27 Elapsed time: 40.481 seconds