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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 03-Jun-2021 02:45:45 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/2_msa/P42898_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/3_mltree/P42898.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/4_raxmlng_ancestral/P42898 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677545
  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/P42898/2_msa/P42898_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 656 sites

WARNING: Sequences tr_J3K515_J3K515_COCIM_246410 and tr_A0A0J6YI68_A0A0J6YI68_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QPH8_B6QPH8_TALMQ_441960 and tr_A0A093V657_A0A093V657_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WMV1_B2WMV1_PYRTR_426418 and tr_A0A2W1GE51_A0A2W1GE51_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6Y9_A0A2I2Y6Y9_GORGO_9595 and sp_P42898_MTHR_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G2WQ21_G2WQ21_VERDV_498257 and tr_A0A0G4M6R1_A0A0G4M6R1_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_B8NG74_B8NG74_ASPFN_332952 and tr_Q2UEQ8_Q2UEQ8_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_F9FK60_F9FK60_FUSOF_660025 and tr_X0CIP6_X0CIP6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FK60_F9FK60_FUSOF_660025 and tr_A0A2H3T9Z5_A0A2H3T9Z5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FK60_F9FK60_FUSOF_660025 and tr_A0A2H3HM20_A0A2H3HM20_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A2QCE3_A2QCE3_ASPNC_425011 and tr_G3Y2A7_G3Y2A7_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QCE3_A2QCE3_ASPNC_425011 and tr_A0A319B7Z7_A0A319B7Z7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7CI98_F7CI98_MACMU_9544 and tr_G8F4Z9_G8F4Z9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7X5I8_G7X5I8_ASPKW_1033177 and tr_A0A146FKQ5_A0A146FKQ5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2XNC0_A2XNC0_ORYSI_39946 and tr_A0A0D3FQL2_A0A0D3FQL2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A2XNC0_A2XNC0_ORYSI_39946 and tr_A0A0D9ZEX1_A0A0D9ZEX1_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2XNC0_A2XNC0_ORYSI_39946 and sp_Q75HE6_MTHR_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4P4P0_F4P4P0_BATDJ_684364 and tr_A0A177WGA5_A0A177WGA5_BATDE_403673 are exactly identical!
WARNING: Sequences tr_G2YUL6_G2YUL6_BOTF4_999810 and tr_M7UVH6_M7UVH6_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_E3MN18_E3MN18_CAERE_31234 and tr_A0A261C7W8_A0A261C7W8_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_F2SQ86_F2SQ86_TRIRC_559305 and tr_A0A178EWV6_A0A178EWV6_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_V2XY75_V2XY75_MONRO_1381753 and tr_A0A0W0EWV1_A0A0W0EWV1_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QTM7_W2QTM7_PHYPN_761204 and tr_A0A0W8DNI6_A0A0W8DNI6_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QTM7_W2QTM7_PHYPN_761204 and tr_W2P2L7_W2P2L7_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RBR0_W2RBR0_PHYPN_761204 and tr_W2NNH0_W2NNH0_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015JXC9_A0A015JXC9_9GLOM_1432141 and tr_A0A2H5T4A6_A0A2H5T4A6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0A1P7C9_A0A0A1P7C9_9FUNG_58291 and tr_A0A367J3J2_A0A367J3J2_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A101MAN1_A0A101MAN1_9EURO_48697 and tr_A0A1V6NRU8_A0A1V6NRU8_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A1S3X4U8_A0A1S3X4U8_TOBAC_4097 and tr_A0A1U7WYR3_A0A1U7WYR3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2S7QR35_A0A2S7QR35_9HELO_2070414 and tr_A0A2S7PJA2_A0A2S7PJA2_9HELO_2070412 are exactly identical!
WARNING: Sequences tr_A0A2U3UZ83_A0A2U3UZ83_TURTR_9739 and tr_A0A2U4AZR3_A0A2U4AZR3_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A319CRF5_A0A319CRF5_9EURO_1448315 and tr_A0A2V5IDG9_A0A2V5IDG9_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 31

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/P42898/4_raxmlng_ancestral/P42898.raxml.reduced.phy

Alignment comprises 1 partitions and 656 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 656
Gaps: 13.08 %
Invariant sites: 0.76 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/4_raxmlng_ancestral/P42898.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/P42898/3_mltree/P42898.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 164 / 13120
[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: -269995.098652

[00:00:00 -269995.098652] Initial branch length optimization
[00:00:01 -269688.906386] Model parameter optimization (eps = 0.100000)

[00:00:30] Tree #1, final logLikelihood: -269147.908224


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.214412,0.232004) (0.232506,0.388660) (0.284546,0.878909) (0.268536,2.270835) 
   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/P42898/4_raxmlng_ancestral/P42898.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/4_raxmlng_ancestral/P42898.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/4_raxmlng_ancestral/P42898.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42898/4_raxmlng_ancestral/P42898.raxml.log

Analysis started: 03-Jun-2021 02:45:45 / finished: 03-Jun-2021 02:46:21

Elapsed time: 36.142 seconds

Consumed energy: 2.777 Wh