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 02-Jun-2021 15:19:51 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/2_msa/P30084_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/3_mltree/P30084.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/4_raxmlng_ancestral/P30084 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636391 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/P30084/2_msa/P30084_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 290 sites WARNING: Sequences tr_B4QEU7_B4QEU7_DROSI_7240 and tr_B4HQX7_B4HQX7_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KD95_J3KD95_COCIM_246410 and tr_A0A0J6YCC2_A0A0J6YCC2_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QP15_B6QP15_TALMQ_441960 and tr_A0A093VN83_A0A093VN83_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WEG2_B2WEG2_PYRTR_426418 and tr_A0A2W1HKP9_A0A2W1HKP9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G2WXD1_G2WXD1_VERDV_498257 and tr_A0A0G4MH28_A0A0G4MH28_9PEZI_100787 are exactly identical! WARNING: Sequences tr_B8NAY6_B8NAY6_ASPFN_332952 and tr_A0A0F0I0C3_A0A0F0I0C3_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NAY6_B8NAY6_ASPFN_332952 and tr_A0A1S9DDA7_A0A1S9DDA7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NAY6_B8NAY6_ASPFN_332952 and tr_A0A2G7G7K7_A0A2G7G7K7_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UWS2_A0A179UWS2_BLAGS_559298 and tr_C5GSP9_C5GSP9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9F776_F9F776_FUSOF_660025 and tr_X0CYV1_X0CYV1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FB61_F9FB61_FUSOF_660025 and tr_A0A0D2XDZ5_A0A0D2XDZ5_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FB61_F9FB61_FUSOF_660025 and tr_N4TYT4_N4TYT4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FB61_F9FB61_FUSOF_660025 and tr_X0D2T3_X0D2T3_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FB61_F9FB61_FUSOF_660025 and tr_A0A2H3TJC3_A0A2H3TJC3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FB61_F9FB61_FUSOF_660025 and tr_A0A2H3H5Y0_A0A2H3H5Y0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9F111_E9F111_METRA_655844 and tr_A0A0B4IDU9_A0A0B4IDU9_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9F111_E9F111_METRA_655844 and tr_A0A0D9NUL8_A0A0D9NUL8_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HHD7_C6HHD7_AJECH_544712 and tr_F0URP0_F0URP0_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4WKH7_J4WKH7_BEAB2_655819 and tr_A0A167J8T2_A0A167J8T2_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_J4WKH7_J4WKH7_BEAB2_655819 and tr_A0A2N6NPL9_A0A2N6NPL9_BEABA_176275 are exactly identical! WARNING: Sequences tr_A2QCA2_A2QCA2_ASPNC_425011 and tr_G3Y271_G3Y271_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7X5M8_G7X5M8_ASPKW_1033177 and tr_A0A100I540_A0A100I540_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X5M8_G7X5M8_ASPKW_1033177 and tr_A0A146FK40_A0A146FK40_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X5M8_G7X5M8_ASPKW_1033177 and tr_A0A1L9NAP0_A0A1L9NAP0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_E5SFS7_E5SFS7_TRISP_6334 and tr_A0A0V1DGC3_A0A0V1DGC3_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SFS7_E5SFS7_TRISP_6334 and tr_A0A0V0W8H3_A0A0V0W8H3_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SFS7_E5SFS7_TRISP_6334 and tr_A0A0V0VHB3_A0A0V0VHB3_9BILA_181606 are exactly identical! WARNING: Sequences tr_F4NZY5_F4NZY5_BATDJ_684364 and tr_A0A177WF01_A0A177WF01_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9X6D7_F9X6D7_ZYMTI_336722 and tr_A0A1X7RNH5_A0A1X7RNH5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XRQ6_G2XRQ6_BOTF4_999810 and tr_M7TWX8_M7TWX8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G2YIH4_G2YIH4_BOTF4_999810 and tr_M7UCD1_M7UCD1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SJ23_F2SJ23_TRIRC_559305 and tr_A0A178F1B3_A0A178F1B3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RM37_B3RM37_TRIAD_10228 and tr_A0A369SJI7_A0A369SJI7_9METZ_287889 are exactly identical! WARNING: Sequences tr_W7LXW0_W7LXW0_GIBM7_334819 and tr_A0A365MLZ5_A0A365MLZ5_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A0A0D2XBY5_A0A0D2XBY5_FUSO4_426428 and tr_A0A2H3H5P0_A0A2H3H5P0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F2PGQ8_F2PGQ8_TRIEC_559882 and tr_A0A059J683_A0A059J683_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L2G0E9_L2G0E9_COLFN_1213859 and tr_T0JX55_T0JX55_COLGC_1237896 are exactly identical! WARNING: Sequences tr_R1DW88_R1DW88_EMIHU_2903 and tr_R1E7G3_R1E7G3_EMIHU_2903 are exactly identical! WARNING: Sequences tr_U5HIX2_U5HIX2_USTV1_683840 and tr_A0A2X0PA43_A0A2X0PA43_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2RFJ7_W2RFJ7_PHYPN_761204 and tr_W2LE88_W2LE88_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A010R8M9_A0A010R8M9_9PEZI_1445577 and tr_A0A135S3M7_A0A135S3M7_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A015KN82_A0A015KN82_9GLOM_1432141 and tr_A0A2I1GGU2_A0A2I1GGU2_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015KN82_A0A015KN82_9GLOM_1432141 and tr_A0A2H5RKN0_A0A2H5RKN0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094E9E6_A0A094E9E6_9PEZI_1420912 and tr_A0A2P2SWC7_A0A2P2SWC7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F9XB95_A0A0F9XB95_TRIHA_5544 and tr_A0A2T4AQX0_A0A2T4AQX0_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8V3W5_A0A0F8V3W5_9EURO_308745 and tr_A0A2T5LSU3_A0A2T5LSU3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1MLV9_A0A0A1MLV9_9FUNG_58291 and tr_A0A367JXN7_A0A367JXN7_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1P1J0_A0A0A1P1J0_9FUNG_58291 and tr_A0A367JC71_A0A367JC71_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0D2GYQ1_A0A0D2GYQ1_9EURO_1442371 and tr_A0A178ZIZ8_A0A178ZIZ8_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A0V1LTV6_A0A0V1LTV6_9BILA_6335 and tr_A0A0V1P0W2_A0A0V1P0W2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A164UUL4_A0A164UUL4_9HOMO_1314777 and tr_A0A166HG15_A0A166HG15_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A2H3BTT2_A0A2H3BTT2_9AGAR_1076256 and tr_A0A284QMT1_A0A284QMT1_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 52 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/P30084/4_raxmlng_ancestral/P30084.raxml.reduced.phy Alignment comprises 1 partitions and 290 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 290 Gaps: 9.81 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/4_raxmlng_ancestral/P30084.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/P30084/3_mltree/P30084.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 73 / 5840 [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: -140976.505640 [00:00:00 -140976.505640] Initial branch length optimization [00:00:01 -140667.906278] Model parameter optimization (eps = 0.100000) [00:00:51] Tree #1, final logLikelihood: -139889.069759 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.254360,0.386652) (0.264818,0.440483) (0.229197,0.942288) (0.251625,2.261439) 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/P30084/4_raxmlng_ancestral/P30084.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/4_raxmlng_ancestral/P30084.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/4_raxmlng_ancestral/P30084.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P30084/4_raxmlng_ancestral/P30084.raxml.log Analysis started: 02-Jun-2021 15:19:51 / finished: 02-Jun-2021 15:20:45 Elapsed time: 54.008 seconds