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 14:18:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/2_msa/Q9GZT5_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/3_mltree/Q9GZT5.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/4_raxmlng_ancestral/Q9GZT5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805530 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/Q9GZT5/2_msa/Q9GZT5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 417 sites WARNING: Sequences tr_B4Q5E7_B4Q5E7_DROSI_7240 and tr_B4HY51_B4HY51_DROSE_7238 are exactly identical! WARNING: Sequences sp_P49337_WNT4_CHICK_9031 and tr_A0A2I0LQU6_A0A2I0LQU6_COLLI_8932 are exactly identical! WARNING: Sequences sp_P49337_WNT4_CHICK_9031 and tr_A0A1V4KRB6_A0A1V4KRB6_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q2LMP1_WNT3A_CHICK_9031 and tr_A0A0Q3USL9_A0A0Q3USL9_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q3C2H6_Q3C2H6_CHICK_9031 and tr_G1NFU4_G1NFU4_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q3C2H6_Q3C2H6_CHICK_9031 and tr_A0A226PAQ0_A0A226PAQ0_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_G3UT87_G3UT87_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_H0ZNI9_H0ZNI9_TAEGU_59729 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_R0M2F0_R0M2F0_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A151P6S2_A0A151P6S2_ALLMI_8496 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A091F4W7_A0A091F4W7_CORBR_85066 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A091IUH6_A0A091IUH6_EGRGA_188379 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A093Q4D8_A0A093Q4D8_9PASS_328815 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A091V0W5_A0A091V0W5_NIPNI_128390 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A093HNM5_A0A093HNM5_STRCA_441894 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A099Z5M2_A0A099Z5M2_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A091GB14_A0A091GB14_9AVES_55661 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A0A0A4S5_A0A0A0A4S5_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q3L254_WNT7B_CHICK_9031 and tr_A0A091IJD2_A0A091IJD2_CALAN_9244 are exactly identical! WARNING: Sequences tr_Q60GF6_Q60GF6_CHICK_9031 and tr_A0A226NNY1_A0A226NNY1_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q60GF6_Q60GF6_CHICK_9031 and tr_A0A226PBI7_A0A226PBI7_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_G1N1F7_G1N1F7_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_K7GBT2_K7GBT2_PELSI_13735 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_R0LCX9_R0LCX9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A151MZI1_A0A151MZI1_ALLMI_8496 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A091J2U4_A0A091J2U4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A093QB31_A0A093QB31_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A093I2C9_A0A093I2C9_STRCA_441894 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A091GE75_A0A091GE75_9AVES_55661 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A1V4JIA4_A0A1V4JIA4_PATFA_372326 are exactly identical! WARNING: Sequences tr_Q9DEB8_Q9DEB8_CHICK_9031 and tr_A0A218UAX8_A0A218UAX8_9PASE_299123 are exactly identical! WARNING: Sequences sp_P17553_WNT3_MOUSE_10090 and tr_D3ZCR1_D3ZCR1_RAT_10116 are exactly identical! WARNING: Sequences sp_P24383_WNT7A_MOUSE_10090 and tr_M0R9D3_M0R9D3_RAT_10116 are exactly identical! WARNING: Sequences sp_P24383_WNT7A_MOUSE_10090 and tr_A0A286Y545_A0A286Y545_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YXS1_M3YXS1_MUSPF_9669 and tr_G1L9Q5_G1L9Q5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YXS1_M3YXS1_MUSPF_9669 and tr_A0A2Y9L0P9_A0A2Y9L0P9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_J9P2Q5_J9P2Q5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_A0A287AGQ6_A0A287AGQ6_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_G1LSD5_G1LSD5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_A0A337SC28_A0A337SC28_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_A0A2Y9M7V7_A0A2Y9M7V7_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z0P4_M3Z0P4_MUSPF_9669 and tr_A0A2Y9SVM9_A0A2Y9SVM9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2M976_H2M976_ORYLA_8090 and tr_I3KPD1_I3KPD1_ORENI_8128 are exactly identical! WARNING: Sequences tr_A0A2I3G281_A0A2I3G281_NOMLE_61853 and tr_H2N3H7_H2N3H7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G281_A0A2I3G281_NOMLE_61853 and tr_H2R817_H2R817_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G281_A0A2I3G281_NOMLE_61853 and sp_P56704_WNT3A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_H2NTP4_H2NTP4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_H2QD96_H2QD96_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_I3N860_I3N860_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and sp_P56703_WNT3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_F7H7P8_F7H7P8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_A0A096P676_A0A096P676_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_A0A2K6E4M9_A0A2K6E4M9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_A0A2K6AII3_A0A2K6AII3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QYC8_G1QYC8_NOMLE_61853 and tr_A0A2R9BL18_A0A2R9BL18_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2I2YNF6_A0A2I2YNF6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2J8LMI4_A0A2J8LMI4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A1D5R803_A0A1D5R803_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2I3LY45_A0A2I3LY45_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A1U7U421_A0A1U7U421_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2K5P8L3_A0A2K5P8L3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2K6BRK5_A0A2K6BRK5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RTL0_G1RTL0_NOMLE_61853 and tr_A0A2R9BAW6_A0A2R9BAW6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1Q5C1_G1Q5C1_MYOLU_59463 and tr_F1N5R1_F1N5R1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I2Z2N4_A0A2I2Z2N4_GORGO_9595 and tr_H2Q569_H2Q569_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z2N4_A0A2I2Z2N4_GORGO_9595 and tr_A0A2R8ZJI6_A0A2R8ZJI6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QM25_G3QM25_GORGO_9595 and tr_H2N6D1_H2N6D1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QM25_G3QM25_GORGO_9595 and tr_H2RAM0_H2RAM0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QM25_G3QM25_GORGO_9595 and sp_Q93097_WNT2B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QM25_G3QM25_GORGO_9595 and tr_A0A2R8ZR94_A0A2R8ZR94_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_J9P5H0_J9P5H0_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A2I3SW84_A0A2I3SW84_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_I3N8I5_I3N8I5_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_H0WWV7_H0WWV7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A286XD12_A0A286XD12_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and sp_P41221_WNT5A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_F7I9H1_F7I9H1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A337SEF3_A0A337SEF3_FELCA_9685 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A1U7U2S8_A0A1U7U2S8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A2U3WDJ1_A0A2U3WDJ1_ODORO_9708 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A2U3YBU5_A0A2U3YBU5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G3QWY6_G3QWY6_GORGO_9595 and tr_A0A2Y9IZJ9_A0A2Y9IZJ9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R6M5_G3R6M5_GORGO_9595 and tr_A0A2J8LQ46_A0A2J8LQ46_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6M5_G3R6M5_GORGO_9595 and sp_O00744_WN10B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_A0A2J8LQ70_A0A2J8LQ70_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and sp_P04628_WNT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_F7IG80_F7IG80_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_A0A096NZ21_A0A096NZ21_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_A0A0D9R1M5_A0A0D9R1M5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_A0A2K6E2D5_A0A2K6E2D5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R6M9_G3R6M9_GORGO_9595 and tr_A0A2R8ZPY6_A0A2R8ZPY6_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q1KYK7_WNT7A_GORGO_9595 and sp_Q1KYL1_WNT7A_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q1KYK7_WNT7A_GORGO_9595 and tr_H0XME5_H0XME5_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q1KYK7_WNT7A_GORGO_9595 and sp_O00755_WNT7A_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q1KYK7_WNT7A_GORGO_9595 and sp_Q1KYK6_WNT7A_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q1KYK7_WNT7A_GORGO_9595 and tr_A0A2R9AAY7_A0A2R9AAY7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8SYT3_A0A2J8SYT3_PONAB_9601 and tr_G7PHR7_G7PHR7_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and tr_K7BKB4_K7BKB4_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and sp_P56705_WNT4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and tr_A0A096MUY0_A0A096MUY0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and tr_A0A0D9S8A8_A0A0D9S8A8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and tr_A0A2U3WRA0_A0A2U3WRA0_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2N8P1_H2N8P1_PONAB_9601 and tr_A0A2Y9KBR1_A0A2Y9KBR1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2P4S1_H2P4S1_PONAB_9601 and sp_P56706_WNT7B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P4S1_H2P4S1_PONAB_9601 and tr_A0A0D9QZ47_A0A0D9QZ47_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2P4S1_H2P4S1_PONAB_9601 and tr_A0A2K5ZBV8_A0A2K5ZBV8_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q27Q52_WNT5A_RABIT_9986 and tr_A0A1S3GC24_A0A1S3GC24_DIPOR_10020 are exactly identical! WARNING: Sequences tr_E2RTG8_E2RTG8_CANLF_9615 and tr_A0A2U3VZE6_A0A2U3VZE6_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RTG8_E2RTG8_CANLF_9615 and tr_A0A2U3XCV6_A0A2U3XCV6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H2QJF8_H2QJF8_PANTR_9598 and sp_Q9GZT5_WN10A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QJF8_H2QJF8_PANTR_9598 and tr_A0A096NRV9_A0A096NRV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QJF8_H2QJF8_PANTR_9598 and tr_A0A2K5NGW5_A0A2K5NGW5_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QJF8_H2QJF8_PANTR_9598 and tr_A0A2K5ZT80_A0A2K5ZT80_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Y115_F6Y115_HORSE_9796 and tr_A0A2Y9KP51_A0A2Y9KP51_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F7A992_F7A992_HORSE_9796 and tr_F1MZV4_F1MZV4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5QSF1_A0A3B5QSF1_XIPMA_8083 and tr_A0A087YIM6_A0A087YIM6_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZUA7_M3ZUA7_XIPMA_8083 and tr_A0A087Y3L2_A0A087Y3L2_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4A0Z7_M4A0Z7_XIPMA_8083 and tr_A0A087X5H9_A0A087X5H9_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088A2N0_A0A088A2N0_APIME_7460 and tr_A0A2A3E709_A0A2A3E709_APICC_94128 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_G7NYG1_G7NYG1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_A0A096MZK6_A0A096MZK6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_A0A0D9RAP9_A0A0D9RAP9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_A0A2K5M3U8_A0A2K5M3U8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_A0A2K6CWS8_A0A2K6CWS8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HEW6_F7HEW6_MACMU_9544 and tr_A0A2K6A9A6_A0A2K6A9A6_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5SUA9_E5SUA9_TRISP_6334 and tr_A0A0V0RP40_A0A0V0RP40_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SUA9_E5SUA9_TRISP_6334 and tr_A0A0V0WJG7_A0A0V0WJG7_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SUA9_E5SUA9_TRISP_6334 and tr_A0A0V1L886_A0A0V1L886_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SUA9_E5SUA9_TRISP_6334 and tr_A0A0V0UBF0_A0A0V0UBF0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_G1LC69_G1LC69_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A337SKL4_A0A337SKL4_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A2U4C3D6_A0A2U4C3D6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A2U3WPR8_A0A2U3WPR8_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A2Y9PFS7_A0A2Y9PFS7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A2Y9TB72_A0A2Y9TB72_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A287AS32_A0A287AS32_PIG_9823 and tr_A0A383ZLD2_A0A383ZLD2_BALAS_310752 are exactly identical! WARNING: Sequences tr_I3LVH1_I3LVH1_PIG_9823 and tr_A0A2Y9T2Y5_A0A2Y9T2Y5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G7NW63_G7NW63_MACFA_9541 and tr_A0A096N474_A0A096N474_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NW63_G7NW63_MACFA_9541 and tr_A0A2K6CVG6_A0A2K6CVG6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NW63_G7NW63_MACFA_9541 and tr_A0A2K5YNF7_A0A2K5YNF7_MANLE_9568 are exactly identical! WARNING: Sequences tr_L5K8A3_L5K8A3_PTEAL_9402 and tr_M3X076_M3X076_FELCA_9685 are exactly identical! WARNING: Sequences tr_L5K8A3_L5K8A3_PTEAL_9402 and tr_A0A1S3AAP9_A0A1S3AAP9_ERIEU_9365 are exactly identical! WARNING: Sequences tr_U3JNI4_U3JNI4_FICAL_59894 and tr_A0A1V4K6B9_A0A1V4K6B9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A096MZI2_A0A096MZI2_PAPAN_9555 and tr_A0A0D9R1M6_A0A0D9R1M6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MZI2_A0A096MZI2_PAPAN_9555 and tr_A0A2K5NR96_A0A2K5NR96_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MZI2_A0A096MZI2_PAPAN_9555 and tr_A0A2K6B0H8_A0A2K6B0H8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MZI2_A0A096MZI2_PAPAN_9555 and tr_A0A2K5XPJ0_A0A2K5XPJ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N8H3_A0A096N8H3_PAPAN_9555 and tr_A0A0D9RGU2_A0A0D9RGU2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096N8H3_A0A096N8H3_PAPAN_9555 and tr_A0A2K6CXM0_A0A2K6CXM0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N8H3_A0A096N8H3_PAPAN_9555 and tr_A0A2K5ZGR8_A0A2K5ZGR8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NPC3_A0A096NPC3_PAPAN_9555 and tr_A0A2K5L5D7_A0A2K5L5D7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NPC3_A0A096NPC3_PAPAN_9555 and tr_A0A2K6CV36_A0A2K6CV36_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091E6A1_A0A091E6A1_CORBR_85066 and tr_A0A091VYP1_A0A091VYP1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091E6A1_A0A091E6A1_CORBR_85066 and tr_A0A087QTS5_A0A087QTS5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093SA54_A0A093SA54_9PASS_328815 and tr_A0A091W026_A0A091W026_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093SA54_A0A093SA54_9PASS_328815 and tr_A0A091WA42_A0A091WA42_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093SA54_A0A093SA54_9PASS_328815 and tr_A0A091FX41_A0A091FX41_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UQ91_A0A091UQ91_NIPNI_128390 and tr_A0A087R0V4_A0A087R0V4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UVD2_A0A091UVD2_NIPNI_128390 and tr_A0A087QPJ4_A0A087QPJ4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V0C8_A0A091V0C8_NIPNI_128390 and tr_A0A087QKE0_A0A087QKE0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V0C8_A0A091V0C8_NIPNI_128390 and tr_A0A091WFA9_A0A091WFA9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091V0C8_A0A091V0C8_NIPNI_128390 and tr_A0A0A0ATC6_A0A0A0ATC6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VIL6_A0A091VIL6_NIPNI_128390 and tr_A0A087RIJ8_A0A087RIJ8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VIL6_A0A091VIL6_NIPNI_128390 and tr_A0A099YZJ5_A0A099YZJ5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091VIL6_A0A091VIL6_NIPNI_128390 and tr_A0A091GI88_A0A091GI88_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VIL6_A0A091VIL6_NIPNI_128390 and tr_A0A0A0AZ19_A0A0A0AZ19_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MK67_A0A2I0MK67_COLLI_8932 and tr_A0A1V4K9W8_A0A1V4K9W8_PATFA_372326 are exactly identical! WARNING: Sequences tr_R7VRM6_R7VRM6_COLLI_8932 and tr_A0A1V4KPX1_A0A1V4KPX1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CNL5_A0A0V1CNL5_TRIBR_45882 and tr_A0A0V0UWV8_A0A0V0UWV8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1S3LI95_A0A1S3LI95_SALSA_8030 and tr_A0A060XVU3_A0A060XVU3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1V4JVM5_A0A1V4JVM5_PATFA_372326 and tr_A0A218U9N7_A0A218U9N7_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A226MMC0_A0A226MMC0_CALSU_9009 and tr_A0A226P2Q0_A0A226P2Q0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MNZ1_A0A226MNZ1_CALSU_9009 and tr_A0A226PFE9_A0A226PFE9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V042_A0A2U3V042_TURTR_9739 and tr_A0A2Y9NFI8_A0A2Y9NFI8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V042_A0A2U3V042_TURTR_9739 and tr_A0A2Y9ERJ6_A0A2Y9ERJ6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V042_A0A2U3V042_TURTR_9739 and tr_A0A383ZW49_A0A383ZW49_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BIA1_A0A2U4BIA1_TURTR_9739 and tr_A0A2Y9MBH2_A0A2Y9MBH2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BIA1_A0A2U4BIA1_TURTR_9739 and tr_A0A2Y9F2M4_A0A2Y9F2M4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3W0I8_A0A2U3W0I8_ODORO_9708 and tr_A0A2U3Z0C2_A0A2U3Z0C2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3YLB3_A0A2U3YLB3_LEPWE_9713 and tr_A0A383ZJ62_A0A383ZJ62_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9N9A7_A0A2Y9N9A7_DELLE_9749 and tr_A0A2Y9ER80_A0A2Y9ER80_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 181 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/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.raxml.reduced.phy Alignment comprises 1 partitions and 417 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 417 Gaps: 21.82 % Invariant sites: 4.56 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.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/Q9GZT5/3_mltree/Q9GZT5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 105 / 8400 [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: -86125.033022 [00:00:00 -86125.033022] Initial branch length optimization [00:00:01 -79359.204434] Model parameter optimization (eps = 0.100000) [00:00:28] Tree #1, final logLikelihood: -79146.056579 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.170875,0.142216) (0.194076,0.247211) (0.405198,0.895076) (0.229852,2.458276) 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/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZT5/4_raxmlng_ancestral/Q9GZT5.raxml.log Analysis started: 04-Jun-2021 14:18:50 / finished: 04-Jun-2021 14:19:22 Elapsed time: 32.436 seconds