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 04-Jun-2021 14:04:58 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/2_msa/Q96QS6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/3_mltree/Q96QS6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/4_raxmlng_ancestral/Q96QS6 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804698 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/Q96QS6/2_msa/Q96QS6_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 385 sites WARNING: Sequences sp_Q8BW96_KCC1D_MOUSE_10090 and tr_I3LNH4_I3LNH4_PIG_9823 are exactly identical! WARNING: Sequences sp_Q8BW96_KCC1D_MOUSE_10090 and tr_A0A2U4B6J6_A0A2U4B6J6_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8BW96_KCC1D_MOUSE_10090 and tr_A0A2Y9T4S3_A0A2Y9T4S3_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8BW96_KCC1D_MOUSE_10090 and tr_A0A383YXR9_A0A383YXR9_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q91VB2_KCC1G_MOUSE_10090 and sp_Q7TNJ7_KCC1G_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_F1PD00_F1PD00_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_G1MH77_G1MH77_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_M3WLG6_M3WLG6_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_A0A2U3WJZ8_A0A2U3WJZ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_A0A2Y9KQC2_A0A2Y9KQC2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YXI3_M3YXI3_MUSPF_9669 and tr_A0A2Y9IEL1_A0A2Y9IEL1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_G3RDE0_G3RDE0_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_A0A2J8VV49_A0A2J8VV49_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_H2QBD1_H2QBD1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and sp_P11801_KPSH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_F7HN09_F7HN09_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_G7Q1F3_G7Q1F3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_A0A096N2R9_A0A096N2R9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QYP3_G1QYP3_NOMLE_61853 and tr_A0A2R8ZTT0_A0A2R8ZTT0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_H2PG90_H2PG90_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A2J8KIU8_A0A2J8KIU8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and sp_Q16566_KCC4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_H9ER84_H9ER84_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A096N9Y8_A0A096N9Y8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A0D9RR33_A0A0D9RR33_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A2K5M5V2_A0A2K5M5V2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A2K6BPX3_A0A2K6BPX3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A2K5Z2Q8_A0A2K5Z2Q8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RL45_G1RL45_NOMLE_61853 and tr_A0A2R9C7Q5_A0A2R9C7Q5_PANPA_9597 are exactly identical! WARNING: Sequences tr_B6QRD7_B6QRD7_TALMQ_441960 and tr_A0A093UXW9_A0A093UXW9_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A2I3T8Y2_A0A2I3T8Y2_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and sp_Q63450_KCC1A_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_I3LZS2_I3LZS2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_F7B069_F7B069_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A2R8MBB6_A0A2R8MBB6_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_G7NYU8_G7NYU8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A096MM11_A0A096MM11_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A2K5L9M2_A0A2K5L9M2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A2K6CMZ2_A0A2K6CMZ2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YBK5_A0A2I2YBK5_GORGO_9595 and tr_A0A2R9AX74_A0A2R9AX74_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QFX0_G3QFX0_GORGO_9595 and tr_A0A2J8QVK8_A0A2J8QVK8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFX0_G3QFX0_GORGO_9595 and sp_Q96NX5_KCC1G_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFX0_G3QFX0_GORGO_9595 and tr_A0A2R9CCR5_A0A2R9CCR5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2N9S4_H2N9S4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2Q1M3_H2Q1M3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and sp_Q8IU85_KCC1D_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H9FXH1_H9FXH1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_G3SL66_G3SL66_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_U3DAZ0_U3DAZ0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A096P3F8_A0A096P3F8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K5LSL0_A0A2K5LSL0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K6DCE4_A0A2K6DCE4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2Y9DRE8_A0A2Y9DRE8_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_G7MEP2_G7MEP2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_G7NUP1_G7NUP1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_A0A096NAP5_A0A096NAP5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_A0A0D9RRT3_A0A0D9RRT3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_A0A2K5N4K8_A0A2K5N4K8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_A0A2K6BLD4_A0A2K6BLD4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8V6J6_A0A2J8V6J6_PONAB_9601 and tr_A0A2K6AA90_A0A2K6AA90_MANLE_9568 are exactly identical! WARNING: Sequences tr_Q29CP9_Q29CP9_DROPS_46245 and tr_B4H883_B4H883_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3S2D1_A0A2I3S2D1_PANTR_9598 and tr_A0A2R9AEL1_A0A2R9AEL1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_N4TD80_N4TD80_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_X0CXX4_X0CXX4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_A0A0N1J353_A0A0N1J353_FUSLA_179993 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_A0A1B8B0Z8_A0A1B8B0Z8_FUSPO_36050 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_A0A2H3T150_A0A2H3T150_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_A0A2H3HUL9_A0A2H3HUL9_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FT45_F9FT45_FUSOF_660025 and tr_A0A2K0W7H4_A0A2K0W7H4_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A158NQZ1_A0A158NQZ1_ATTCE_12957 and tr_F4WPE0_F4WPE0_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NQZ1_A0A158NQZ1_ATTCE_12957 and tr_A0A195B0Y3_A0A195B0Y3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2I3MXS4_A0A2I3MXS4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A0D9R3M3_A0A0D9R3M3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2K5NMH2_A0A2K5NMH2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2K6DFZ6_A0A2K6DFZ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2K5XVT4_A0A2K5XVT4_MANLE_9568 are exactly identical! WARNING: Sequences tr_E3LY11_E3LY11_CAERE_31234 and tr_A0A261AUV8_A0A261AUV8_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8Y1H9_A8Y1H9_CAEBR_6238 and tr_A0A2G5VU88_A0A2G5VU88_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B4MF09_B4MF09_DROVI_7244 and tr_D0Z7B0_D0Z7B0_DROVI_7244 are exactly identical! WARNING: Sequences tr_D2H9G2_D2H9G2_AILME_9646 and tr_A0A384D0V7_A0A384D0V7_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3WK93_M3WK93_FELCA_9685 and tr_A0A2U3ZKT5_A0A2U3ZKT5_ODORO_9708 are exactly identical! WARNING: Sequences tr_R0JAC2_R0JAC2_ANAPL_8839 and tr_A0A091FQZ9_A0A091FQZ9_9AVES_55661 are exactly identical! WARNING: Sequences tr_W2Q2T2_W2Q2T2_PHYPN_761204 and tr_A0A0W8DQ77_A0A0W8DQ77_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q2T2_W2Q2T2_PHYPN_761204 and tr_W2GJQ0_W2GJQ0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RD06_W2RD06_PHYPN_761204 and tr_A0A0W8D224_A0A0W8D224_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RD06_W2RD06_PHYPN_761204 and tr_W2J829_W2J829_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015JR60_A0A015JR60_9GLOM_1432141 and tr_A0A2H5T156_A0A2H5T156_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015KDF0_A0A015KDF0_9GLOM_1432141 and tr_U9U8R9_U9U8R9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0K0EX60_A0A0K0EX60_STRVS_75913 and tr_A0A0N5BZG7_A0A0N5BZG7_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0W8C5Z3_A0A0W8C5Z3_PHYNI_4790 and tr_W2JWL5_W2JWL5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091EXY6_A0A091EXY6_CORBR_85066 and tr_A0A093HS28_A0A093HS28_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A093Q1H6_A0A093Q1H6_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A091V724_A0A091V724_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A087RE42_A0A087RE42_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A091WSD8_A0A091WSD8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A099ZB55_A0A099ZB55_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A194R057_A0A194R057_PAPMA_76193 and tr_A0A194PHI5_A0A194PHI5_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A091V194_A0A091V194_NIPNI_128390 and tr_A0A087QNZ5_A0A087QNZ5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091FIZ0_A0A091FIZ0_9AVES_55661 and tr_A0A0A0ADQ5_A0A0A0ADQ5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MH53_A0A2I0MH53_COLLI_8932 and tr_A0A1V4K061_A0A1V4K061_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0L0RZH4_A0A0L0RZH4_ALLMA_578462 and tr_A0A0L0SCH3_A0A0L0SCH3_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V1D7J2_A0A0V1D7J2_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V0WNB5_A0A0V0WNB5_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V0VI16_A0A0V0VI16_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V1A9G1_A0A0V1A9G1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V1NUL9_A0A0V1NUL9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V0TJP0_A0A0V0TJP0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V1D1S3_A0A0V1D1S3_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V0WTZ8_A0A0V0WTZ8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V0VT14_A0A0V0VT14_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V1LIA5_A0A0V1LIA5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V0ZZD4_A0A0V0ZZD4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V1G1G0_A0A0V1G1G0_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V1N479_A0A0V1N479_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V1NYS4_A0A0V1NYS4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S1B4_A0A0V0S1B4_9BILA_6336 and tr_A0A0V0UH07_A0A0V0UH07_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0XXP2_A0A0V0XXP2_TRIPS_6337 and tr_A0A0V1MZA0_A0A0V1MZA0_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0XXP2_A0A0V0XXP2_TRIPS_6337 and tr_A0A0V1HGV5_A0A0V1HGV5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3P3M7_A0A1S3P3M7_SALSA_8030 and tr_B5X2V5_B5X2V5_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MH32_A0A226MH32_CALSU_9009 and tr_A0A226PWN5_A0A226PWN5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NFP1_A0A226NFP1_CALSU_9009 and tr_A0A226PGM3_A0A226PGM3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SKI3_A0A2D0SKI3_ICTPU_7998 and tr_A0A2D0SKI6_A0A2D0SKI6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LMF9_A0A2K5LMF9_CERAT_9531 and tr_A0A2K5XWN6_A0A2K5XWN6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V5L7_A0A2U3V5L7_TURTR_9739 and tr_A0A2Y9Q1D0_A0A2Y9Q1D0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V5L7_A0A2U3V5L7_TURTR_9739 and tr_A0A2Y9EWB4_A0A2Y9EWB4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V5L7_A0A2U3V5L7_TURTR_9739 and tr_A0A383YMH6_A0A383YMH6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BT38_A0A2U4BT38_TURTR_9739 and tr_A0A2Y9PMY3_A0A2Y9PMY3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3Y5T3_A0A2U3Y5T3_LEPWE_9713 and tr_A0A384CMR5_A0A384CMR5_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2Y9P1H6_A0A2Y9P1H6_DELLE_9749 and tr_A0A384BFJ6_A0A384BFJ6_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 129 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/Q96QS6/4_raxmlng_ancestral/Q96QS6.raxml.reduced.phy Alignment comprises 1 partitions and 385 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 385 Gaps: 18.12 % Invariant sites: 1.56 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/4_raxmlng_ancestral/Q96QS6.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/Q96QS6/3_mltree/Q96QS6.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 97 / 7760 [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: -130074.753922 [00:00:00 -130074.753922] Initial branch length optimization [00:00:01 -114840.691865] Model parameter optimization (eps = 0.100000) [00:00:32] Tree #1, final logLikelihood: -114432.149013 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.188904,0.227453) (0.198452,0.265175) (0.355499,0.915703) (0.257145,2.251171) 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/Q96QS6/4_raxmlng_ancestral/Q96QS6.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/4_raxmlng_ancestral/Q96QS6.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/4_raxmlng_ancestral/Q96QS6.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q96QS6/4_raxmlng_ancestral/Q96QS6.raxml.log Analysis started: 04-Jun-2021 14:04:58 / finished: 04-Jun-2021 14:05:34 Elapsed time: 35.977 seconds