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 19-Jul-2021 13:27:10 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/2_msa/Q9NPA2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/3_mltree/Q9NPA2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/4_raxmlng_ancestral/Q9NPA2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626690430 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/Q9NPA2/2_msa/Q9NPA2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 562 sites WARNING: Sequences sp_Q9R0S2_MMP24_MOUSE_10090 and sp_Q99PW6_MMP24_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2I2Y1M9_A0A2I2Y1M9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and sp_P51512_MMP16_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_F6XP71_F6XP71_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_F7G1M2_F7G1M2_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_G7PC63_G7PC63_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2I3MBZ0_A0A2I3MBZ0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A0D9RKH8_A0A0D9RKH8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2K5N2Y6_A0A2K5N2Y6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2K6ANU7_A0A2K6ANU7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2R8ZII6_A0A2R8ZII6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and tr_H2Q7Z4_H2Q7Z4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and sp_P50281_MMP14_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and tr_A0A2R9BFH7_A0A2R9BFH7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S700_G3S700_GORGO_9595 and sp_P51511_MMP15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F1PLV8_F1PLV8_CANLF_9615 and tr_A0A2U3WW95_A0A2U3WW95_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PLV8_F1PLV8_CANLF_9615 and tr_A0A2Y9JAJ2_A0A2Y9JAJ2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_F6RLA7_F6RLA7_HORSE_9796 are exactly identical! WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_L5JXS3_L5JXS3_PTEAL_9402 are exactly identical! WARNING: Sequences tr_H2Q4N2_H2Q4N2_PANTR_9598 and tr_A0A2R9BCT7_A0A2R9BCT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QK91_H2QK91_PANTR_9598 and sp_Q9Y5R2_MMP24_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A096NIY8_A0A096NIY8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K5NGB0_A0A2K5NGB0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K6CWE1_A0A2K6CWE1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_G7P9U2_G7P9U2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A096NSD0_A0A096NSD0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A0D9RUM3_A0A0D9RUM3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K5KJ44_A0A2K5KJ44_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K6BNL4_A0A2K6BNL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K5X9Y4_A0A2K5X9Y4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GQW6_F7GQW6_MACMU_9544 and tr_A0A2K6AZ02_A0A2K6AZ02_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9H3A5_H9H3A5_MACMU_9544 and tr_A0A2K6BT47_A0A2K6BT47_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PGJ0_G7PGJ0_MACFA_9541 and tr_A0A0D9RDJ2_A0A0D9RDJ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PGJ0_G7PGJ0_MACFA_9541 and tr_A0A2K5LI89_A0A2K5LI89_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PNK0_G7PNK0_MACFA_9541 and tr_A0A096NXU1_A0A096NXU1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PNK0_G7PNK0_MACFA_9541 and tr_A0A2K5NYX0_A0A2K5NYX0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PNK0_G7PNK0_MACFA_9541 and tr_A0A2K5YCD5_A0A2K5YCD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_U3JRD6_U3JRD6_FICAL_59894 and tr_A0A091EJH3_A0A091EJH3_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3JRD6_U3JRD6_FICAL_59894 and tr_A0A218V6Q0_A0A218V6Q0_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A091IY01_A0A091IY01_EGRGA_188379 and tr_A0A091VE80_A0A091VE80_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IY01_A0A091IY01_EGRGA_188379 and tr_A0A087QVU2_A0A087QVU2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IY01_A0A091IY01_EGRGA_188379 and tr_A0A0A0AXT1_A0A0A0AXT1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VTZ5_A0A091VTZ5_NIPNI_128390 and tr_A0A091WEJ9_A0A091WEJ9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V1LUQ3_A0A0V1LUQ3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V1AGY6_A0A0V1AGY6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V1NVP9_A0A0V1NVP9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V0UA13_A0A0V0UA13_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2D0T8J0_A0A2D0T8J0_ICTPU_7998 and tr_A0A2D0T8K1_A0A2D0T8K1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K6B6K0_A0A2K6B6K0_MACNE_9545 and tr_A0A2K5Z9B5_A0A2K5Z9B5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9EHE1_A0A2Y9EHE1_PHYCD_9755 and tr_A0A384B0R6_A0A384B0R6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9SX66_A0A2Y9SX66_PHYCD_9755 and tr_A0A384A1W3_A0A384A1W3_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 51 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/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.raxml.reduced.phy Alignment comprises 1 partitions and 562 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 562 Gaps: 17.85 % Invariant sites: 0.89 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.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/Q9NPA2/3_mltree/Q9NPA2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 141 / 11280 [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: -227027.552806 [00:00:00 -227027.552806] Initial branch length optimization [00:00:01 -224030.971448] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -223747.105905 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.119076,0.237688) (0.179467,0.386600) (0.333070,0.824380) (0.368387,1.704019) 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/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NPA2/4_raxmlng_ancestral/Q9NPA2.raxml.log Analysis started: 19-Jul-2021 13:27:10 / finished: 19-Jul-2021 13:27:51 Elapsed time: 40.770 seconds