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 01:58:57 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/2_msa/P00966_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/3_mltree/P00966.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/4_raxmlng_ancestral/P00966 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674737 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/P00966/2_msa/P00966_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 412 sites WARNING: Sequences tr_E3RQL6_E3RQL6_PYRTT_861557 and tr_B2W9Q7_B2W9Q7_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RQL6_E3RQL6_PYRTT_861557 and tr_A0A2W1CQ74_A0A2W1CQ74_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G1RPP0_G1RPP0_NOMLE_61853 and sp_P00966_ASSY_HUMAN_9606 are exactly identical! WARNING: Sequences tr_J3KBA3_J3KBA3_COCIM_246410 and tr_A0A0J7BC14_A0A0J7BC14_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QJF4_B6QJF4_TALMQ_441960 and tr_A0A093UYS4_A0A093UYS4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3R3Z8_G3R3Z8_GORGO_9595 and tr_A0A2R9B7D9_A0A2R9B7D9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2XJW7_G2XJW7_VERDV_498257 and tr_A0A0G4M1X7_A0A0G4M1X7_9PEZI_100787 are exactly identical! WARNING: Sequences tr_B8N8L6_B8N8L6_ASPFN_332952 and tr_Q2UHL9_Q2UHL9_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N8L6_B8N8L6_ASPFN_332952 and tr_A0A1S9DY74_A0A1S9DY74_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_J4UI03_J4UI03_BEAB2_655819 and tr_A0A0A2VFS6_A0A0A2VFS6_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_A2ZJA1_A2ZJA1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_A0A0E0RFD4_A0A0E0RFD4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_A0A0D3HSS7_A0A0D3HSS7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_A0A0E0BQR1_A0A0E0BQR1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_A0A0E0MKX8_A0A0E0MKX8_ORYPU_4537 are exactly identical! WARNING: Sequences tr_A0A0E0J8C8_A0A0E0J8C8_ORYNI_4536 and tr_Q2QVC1_Q2QVC1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2R515_A2R515_ASPNC_425011 and tr_G7XUE7_G7XUE7_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2R515_A2R515_ASPNC_425011 and tr_G3XXV7_G3XXV7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R515_A2R515_ASPNC_425011 and tr_A0A1L9MRY1_A0A1L9MRY1_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2R515_A2R515_ASPNC_425011 and tr_A0A317W0W0_A0A317W0W0_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2R515_A2R515_ASPNC_425011 and tr_A0A319A452_A0A319A452_9EURO_1450533 are exactly identical! WARNING: Sequences tr_H9ESN2_H9ESN2_MACMU_9544 and tr_A0A096P0G1_A0A096P0G1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9ESN2_H9ESN2_MACMU_9544 and tr_A0A2K6E313_A0A2K6E313_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4NWR2_F4NWR2_BATDJ_684364 and tr_A0A177WJB6_A0A177WJB6_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9X4H2_F9X4H2_ZYMTI_336722 and tr_A0A1X7RK06_A0A1X7RK06_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XZJ0_G2XZJ0_BOTF4_999810 and tr_M7V0U7_M7V0U7_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_W7MLY3_W7MLY3_GIBM7_334819 and tr_A0A2K0WV90_A0A2K0WV90_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F2PP65_F2PP65_TRIEC_559882 and tr_A0A059J388_A0A059J388_9EURO_1215338 are exactly identical! WARNING: Sequences tr_S0ENH2_S0ENH2_GIBF5_1279085 and tr_A0A365NGZ9_A0A365NGZ9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M2T526_M2T526_COCSN_665912 and tr_M2UL94_M2UL94_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2T526_M2T526_COCSN_665912 and tr_W6XX90_W6XX90_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2T526_M2T526_COCSN_665912 and tr_W6ZA11_W6ZA11_COCMI_930090 are exactly identical! WARNING: Sequences tr_V2X0P8_V2X0P8_MONRO_1381753 and tr_A0A0W0F578_A0A0W0F578_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PDR0_W2PDR0_PHYPN_761204 and tr_A0A0W8C5J2_A0A0W8C5J2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PDR0_W2PDR0_PHYPN_761204 and tr_W2H3B3_W2H3B3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B5Y2C2_A0A3B5Y2C2_WHEAT_4565 and tr_A0A3B5YYM1_A0A3B5YYM1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015KJH2_A0A015KJH2_9GLOM_1432141 and tr_U9TEH6_U9TEH6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094GUG4_A0A094GUG4_9PEZI_1420912 and tr_A0A1B8GQJ0_A0A1B8GQJ0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_X0DS59_X0DS59_FUSOX_1089458 and tr_A0A2H3HU47_A0A2H3HU47_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A0C9M3W2_A0A0C9M3W2_9FUNG_91626 and tr_A0A168K890_A0A168K890_MUCCL_747725 are exactly identical! WARNING: Sequences tr_A0A0P1BCC8_A0A0P1BCC8_9BASI_401625 and tr_A0A316VZW9_A0A316VZW9_9BASI_1522189 are exactly identical! WARNING: Sequences tr_A0A117NNN6_A0A117NNN6_9EURO_48697 and tr_A0A1V6P264_A0A1V6P264_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A1S3YX56_A0A1S3YX56_TOBAC_4097 and tr_A0A1J6ITI4_A0A1J6ITI4_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3YX56_A0A1S3YX56_TOBAC_4097 and tr_A0A1U7W8P4_A0A1U7W8P4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1B9ITP1_A0A1B9ITP1_9TREE_1331196 and tr_A0A1B9G5D4_A0A1B9G5D4_9TREE_1296100 are exactly identical! WARNING: Sequences tr_A0A1L9WYF6_A0A1L9WYF6_ASPAC_690307 and tr_A0A319CM36_A0A319CM36_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9WYF6_A0A1L9WYF6_ASPAC_690307 and tr_A0A2V5J271_A0A2V5J271_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9WYF6_A0A1L9WYF6_ASPAC_690307 and tr_A0A2V5HG72_A0A2V5HG72_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A1R3RDT4_A0A1R3RDT4_ASPC5_602072 and tr_A0A319ED55_A0A319ED55_9EURO_1448318 are exactly identical! WARNING: Duplicate sequences found: 49 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/P00966/4_raxmlng_ancestral/P00966.raxml.reduced.phy Alignment comprises 1 partitions and 412 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 412 Gaps: 8.40 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/4_raxmlng_ancestral/P00966.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/P00966/3_mltree/P00966.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 103 / 8240 [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: -133744.260883 [00:00:00 -133744.260883] Initial branch length optimization [00:00:01 -133485.867109] Model parameter optimization (eps = 0.100000) [00:00:42] Tree #1, final logLikelihood: -133028.351820 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.250836,0.429998) (0.261855,0.552369) (0.270102,0.947112) (0.217207,2.263661) 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/P00966/4_raxmlng_ancestral/P00966.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/4_raxmlng_ancestral/P00966.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/4_raxmlng_ancestral/P00966.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P00966/4_raxmlng_ancestral/P00966.raxml.log Analysis started: 03-Jun-2021 01:58:57 / finished: 03-Jun-2021 01:59:44 Elapsed time: 46.715 seconds Consumed energy: 3.083 Wh