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 12-Jul-2021 17:53:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/2_msa/Q9UK17_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/3_mltree/Q9UK17.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101580 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/300621_run/phylogeny-snakemake/results/Q9UK17/2_msa/Q9UK17_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 655 sites WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226MDZ7_A0A226MDZ7_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_G1NRG0_G1NRG0_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_U3KJP7_U3KJP7_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_R0L1C6_R0L1C6_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091F1M2_A0A091F1M2_CORBR_85066 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091JJF6_A0A091JJF6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093QHE1_A0A093QHE1_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091WS81_A0A091WS81_NIPNI_128390 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093HKM6_A0A093HKM6_STRCA_441894 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091V9H0_A0A091V9H0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091G9V4_A0A091G9V4_9AVES_55661 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A0A0AYN4_A0A0A0AYN4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A2I0M055_A0A2I0M055_COLLI_8932 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A1V4KWW4_A0A1V4KWW4_PATFA_372326 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A218US50_A0A218US50_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226NIE9_A0A226NIE9_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226PWN8_A0A226PWN8_COLVI_9014 are exactly identical! WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and sp_P63142_KCNA2_RAT_10116 are exactly identical! WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_A0A1U7QPQ5_A0A1U7QPQ5_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_F1PKN8_F1PKN8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_M3W515_M3W515_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_A0A2U3WVM7_A0A2U3WVM7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_F1PBP9_F1PBP9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_F7A2Q7_F7A2Q7_ORNAN_9258 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_W5PQ46_W5PQ46_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_H0XWH0_H0XWH0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and sp_P16389_KCNA2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_G7MIG1_G7MIG1_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_Q1AP78_Q1AP78_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_D2HZL7_D2HZL7_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_G7NW44_G7NW44_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_F1MKB0_F1MKB0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A091DJ88_A0A091DJ88_FUKDA_885580 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A0D9SAD5_A0A0D9SAD5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A1S3A4Y5_A0A1S3A4Y5_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A1S3GEU1_A0A1S3GEU1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2R8ZH38_A0A2R8ZH38_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2Y9IZ48_A0A2Y9IZ48_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8HYZ1_KCND2_MUSPF_9669 and tr_A0A2Y9JXW9_A0A2Y9JXW9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_H2QWA6_H2QWA6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and sp_Q92953_KCNB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A2R9C703_A0A2R9C703_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_G3RHS4_G3RHS4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_H2N6D2_H2N6D2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_H2RI65_H2RI65_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and sp_Q9UK17_KCND3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_G7NW61_G7NW61_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_A0A0D9S6F4_A0A0D9S6F4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_A0A2K6CJ17_A0A2K6CJ17_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_A0A2K6AAE9_A0A2K6AAE9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QVI2_G1QVI2_NOMLE_61853 and tr_A0A2R9BX19_A0A2R9BX19_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R5M2_G1R5M2_NOMLE_61853 and tr_G3QVG8_G3QVG8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R5M2_G1R5M2_NOMLE_61853 and tr_A0A2J8SF99_A0A2J8SF99_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R5M2_G1R5M2_NOMLE_61853 and tr_A0A2J8MJF2_A0A2J8MJF2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5M2_G1R5M2_NOMLE_61853 and sp_Q14721_KCNB1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5M2_G1R5M2_NOMLE_61853 and tr_A0A2R9ADU2_A0A2R9ADU2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_G3QEG2_G3QEG2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_F6UCV5_F6UCV5_MONDO_13616 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_F6XE18_F6XE18_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_I3NB95_I3NB95_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_A0A286XTL3_A0A286XTL3_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_G3VY70_G3VY70_SARHA_9305 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_A0A1U7U342_A0A1U7U342_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3HTC7_G3HTC7_CRIGR_10029 and tr_F6U3G2_F6U3G2_HORSE_9796 are exactly identical! WARNING: Sequences tr_G3HTC7_G3HTC7_CRIGR_10029 and tr_G3T248_G3T248_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G3HTC7_G3HTC7_CRIGR_10029 and tr_A0A1U7TTB8_A0A1U7TTB8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_H2NG69_H2NG69_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_H2Q593_H2Q593_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_F7DS72_F7DS72_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A096N578_A0A096N578_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A0D9SCZ1_A0A0D9SCZ1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K5KMH7_A0A2K5KMH7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K6AM91_A0A2K6AM91_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K5XFR1_A0A2K5XFR1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2R8ZFZ7_A0A2R8ZFZ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RGW7_E2RGW7_CANLF_9615 and tr_A0A2U3Y403_A0A2U3Y403_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H2QYK7_H2QYK7_PANTR_9598 and sp_Q9NSA2_KCND1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QYK7_H2QYK7_PANTR_9598 and tr_A0A2R9B401_A0A2R9B401_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BBB6_K7BBB6_PANTR_9598 and sp_Q9NZV8_KCND2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7BBB6_K7BBB6_PANTR_9598 and tr_A0A2R9B1Q7_A0A2R9B1Q7_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PSR3_W5PSR3_SHEEP_9940 and tr_E1BDC5_E1BDC5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4B0C0_M4B0C0_XIPMA_8083 and tr_A0A087YSG5_A0A087YSG5_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4B0C1_M4B0C1_XIPMA_8083 and tr_A0A087YSG6_A0A087YSG6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A1D5Q0L6_A0A1D5Q0L6_MACMU_9544 and tr_A0A096NNR7_A0A096NNR7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q7Z0_F6Q7Z0_MACMU_9544 and tr_A0A096MKX7_A0A096MKX7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q7Z0_F6Q7Z0_MACMU_9544 and tr_A0A2K5KVE4_A0A2K5KVE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q7Z0_F6Q7Z0_MACMU_9544 and tr_A0A2K5ZDL1_A0A2K5ZDL1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6S4U3_F6S4U3_MACMU_9544 and tr_G7Q2P3_G7Q2P3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S4U3_F6S4U3_MACMU_9544 and tr_A0A096NPF3_A0A096NPF3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6S4U3_F6S4U3_MACMU_9544 and tr_A0A2K6E6Q8_A0A2K6E6Q8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6S4U3_F6S4U3_MACMU_9544 and tr_A0A2K6AIJ7_A0A2K6AIJ7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FAN1_F7FAN1_MACMU_9544 and tr_A0A2I3MMS9_A0A2I3MMS9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FAN1_F7FAN1_MACMU_9544 and tr_A0A1S3FG01_A0A1S3FG01_DIPOR_10020 are exactly identical! WARNING: Sequences tr_F7FAN1_F7FAN1_MACMU_9544 and tr_A0A2K5M744_A0A2K5M744_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FAN1_F7FAN1_MACMU_9544 and tr_A0A2K6AME3_A0A2K6AME3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FAN1_F7FAN1_MACMU_9544 and tr_A0A2K5YH77_A0A2K5YH77_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5BNR2_G5BNR2_HETGA_10181 and tr_L5KR79_L5KR79_PTEAL_9402 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0SI28_A0A0V0SI28_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0X271_A0A0V0X271_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0VUY8_A0A0V0VUY8_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0ZLE5_A0A0V0ZLE5_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V1P110_A0A0V1P110_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0UAJ5_A0A0V0UAJ5_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0YRL3_H0YRL3_TAEGU_59729 and tr_A0A087QMX2_A0A087QMX2_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_U3KKD6_U3KKD6_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A091FNI5_A0A091FNI5_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A093GUI1_A0A093GUI1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A218UFS4_A0A218UFS4_9PASE_299123 are exactly identical! WARNING: Sequences tr_A8WZX5_A8WZX5_CAEBR_6238 and tr_A0A2G5U243_A0A2G5U243_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and sp_Q4ZHA6_KCNB2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A067QL12_A0A067QL12_ZOONE_136037 and tr_A0A2J7PXU2_A0A2J7PXU2_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A0Q3TDE8_A0A0Q3TDE8_AMAAE_12930 and tr_A0A091J9T8_A0A091J9T8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F2Z4_A0A091F2Z4_CORBR_85066 and tr_A0A087QPJ6_A0A087QPJ6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F2Z4_A0A091F2Z4_CORBR_85066 and tr_A0A091HQ73_A0A091HQ73_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091F2Z4_A0A091F2Z4_CORBR_85066 and tr_A0A226MMD5_A0A226MMD5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A091F2Z4_A0A091F2Z4_CORBR_85066 and tr_A0A226PXM5_A0A226PXM5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A091J2L1_A0A091J2L1_EGRGA_188379 and tr_A0A091UMT2_A0A091UMT2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JQX9_A0A091JQX9_EGRGA_188379 and tr_A0A091VQM5_A0A091VQM5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JUX1_A0A091JUX1_EGRGA_188379 and tr_A0A091UZ01_A0A091UZ01_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JUX1_A0A091JUX1_EGRGA_188379 and tr_A0A0A0AFE4_A0A0A0AFE4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JUX1_A0A091JUX1_EGRGA_188379 and tr_A0A093GJZ2_A0A093GJZ2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091UW60_A0A091UW60_NIPNI_128390 and tr_A0A087QPJ7_A0A087QPJ7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UW60_A0A091UW60_NIPNI_128390 and tr_A0A091G2W1_A0A091G2W1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UW60_A0A091UW60_NIPNI_128390 and tr_A0A0A0ASM0_A0A0A0ASM0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087RJT1_A0A087RJT1_APTFO_9233 and tr_A0A091XL48_A0A091XL48_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A087RJT1_A0A087RJT1_APTFO_9233 and tr_A0A099ZVZ5_A0A099ZVZ5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A099Z0H5_A0A099Z0H5_TINGU_94827 and tr_A0A226N7J6_A0A226N7J6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A099Z0H5_A0A099Z0H5_TINGU_94827 and tr_A0A226PM26_A0A226PM26_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A099Z651_A0A099Z651_TINGU_94827 and tr_A0A091ID14_A0A091ID14_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0A0AQ41_A0A0A0AQ41_CHAVO_50402 and tr_A0A093I3M2_A0A093I3M2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2I0MKC3_A0A2I0MKC3_COLLI_8932 and tr_A0A1V4K8E8_A0A1V4K8E8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CYR3_A0A0V1CYR3_TRIBR_45882 and tr_A0A0V0VPW1_A0A0V0VPW1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CYR3_A0A0V1CYR3_TRIBR_45882 and tr_A0A0V0U9A3_A0A0V0U9A3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WDR1_A0A0V0WDR1_9BILA_92179 and tr_A0A0V0ZY78_A0A0V0ZY78_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0WDR1_A0A0V0WDR1_9BILA_92179 and tr_A0A0V1NZG4_A0A0V1NZG4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3LFL4_A0A1S3LFL4_SALSA_8030 and tr_A0A060Y414_A0A060Y414_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3LGM5_A0A1S3LGM5_SALSA_8030 and tr_A0A060YTH8_A0A060YTH8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2U3V2M1_A0A2U3V2M1_TURTR_9739 and tr_A0A2Y9P953_A0A2Y9P953_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V2M1_A0A2U3V2M1_TURTR_9739 and tr_A0A2Y9EPE4_A0A2Y9EPE4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4B057_A0A2U4B057_TURTR_9739 and tr_A0A2Y9NT69_A0A2Y9NT69_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WF03_A0A2U3WF03_ODORO_9708 and tr_A0A2Y9J1U9_A0A2Y9J1U9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3WF14_A0A2U3WF14_ODORO_9708 and tr_A0A2U3XN46_A0A2U3XN46_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9SE91_A0A2Y9SE91_PHYCD_9755 and tr_A0A383Z2Z6_A0A383Z2Z6_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 143 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.raxml.reduced.phy Alignment comprises 1 partitions and 655 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 655 Gaps: 28.51 % Invariant sites: 1.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.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/300621_run/phylogeny-snakemake/results/Q9UK17/3_mltree/Q9UK17.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: -127667.493868 [00:00:00 -127667.493868] Initial branch length optimization [00:00:01 -127049.516605] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -126587.725713 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.198607,0.190392) (0.191473,0.275082) (0.279920,0.667817) (0.330000,2.189638) 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/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UK17/4_raxmlng_ancestral/Q9UK17.raxml.log Analysis started: 12-Jul-2021 17:53:00 / finished: 12-Jul-2021 17:53:58 Elapsed time: 58.269 seconds Consumed energy: 4.882 Wh