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 13:34:15 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/2_msa/Q9BZS1_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/3_mltree/Q9BZS1.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/4_raxmlng_ancestral/Q9BZS1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802855 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/Q9BZS1/2_msa/Q9BZS1_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 431 sites WARNING: Sequences tr_E1BTL6_E1BTL6_CHICK_9031 and tr_U3J1G2_U3J1G2_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1BTL6_E1BTL6_CHICK_9031 and tr_A0A099Z5E2_A0A099Z5E2_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q61850_FOXC2_MOUSE_10090 and sp_Q63246_FOXC2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61850_FOXC2_MOUSE_10090 and tr_A0A1U7QG24_A0A1U7QG24_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A2J8Y5W7_A0A2J8Y5W7_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_G1T1P6_G1T1P6_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A2I3TI48_A0A2I3TI48_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_F6SCJ5_F6SCJ5_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_I3MAE8_I3MAE8_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and sp_Q9UPW0_FOXJ3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_F7C0R5_F7C0R5_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_U3BLV8_U3BLV8_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A096MKU3_A0A096MKU3_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A0D9S7L3_A0A0D9S7L3_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A1S3F705_A0A1S3F705_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A2K5M1J1_A0A2K5M1J1_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A2K6CJU0_A0A2K6CJU0_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q8BUR3_FOXJ3_MOUSE_10090 and tr_A0A2K5YRN4_A0A2K5YRN4_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_H2NUS8_H2NUS8_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_H2QDX6_H2QDX6_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and sp_Q92949_FOXJ1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_F1RWM7_F1RWM7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_E1BNF3_E1BNF3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_A0A2U3VHQ8_A0A2U3VHQ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_A0A2U3X9J3_A0A2U3X9J3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YQ11_M3YQ11_MUSPF_9669 and tr_A0A2Y9L1K2_A0A2Y9L1K2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_G1P3E4_G1P3E4_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_F7DC87_F7DC87_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_W5NWJ0_W5NWJ0_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_G3SRH1_G3SRH1_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_E1B8C0_E1B8C0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_A0A2U3WG44_A0A2U3WG44_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_A0A2U3Y3L0_A0A2U3Y3L0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_A0A2Y9KYD5_A0A2Y9KYD5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_A0A2Y9NGM8_A0A2Y9NGM8_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YZ76_M3YZ76_MUSPF_9669 and tr_A0A2Y9T571_A0A2Y9T571_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YZY5_M3YZY5_MUSPF_9669 and tr_F1PY16_F1PY16_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3GUK3_A0A2I3GUK3_NOMLE_61853 and tr_G3R4E1_G3R4E1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GUK3_A0A2I3GUK3_NOMLE_61853 and tr_A0A2I3SFB7_A0A2I3SFB7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GUK3_A0A2I3GUK3_NOMLE_61853 and tr_A0A2I3MGC1_A0A2I3MGC1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GUK3_A0A2I3GUK3_NOMLE_61853 and tr_A0A2K6BAR7_A0A2K6BAR7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HZR2_A0A2I3HZR2_NOMLE_61853 and tr_A0A2I2Z6P5_A0A2I2Z6P5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_H2NGE0_H2NGE0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_H2Q5D1_H2Q5D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_G7N5W4_G7N5W4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_F7IKN2_F7IKN2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_G7PJQ2_G7PJQ2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_A0A096MYM0_A0A096MYM0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_A0A0D9RBK6_A0A0D9RBK6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_A0A2K5LY45_A0A2K5LY45_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_A0A2K6AV93_A0A2K6AV93_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QMA0_G1QMA0_NOMLE_61853 and tr_A0A2R9C3N6_A0A2R9C3N6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and sp_Q8MJ99_FOXP2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_F1PFY7_F1PFY7_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_A0A2I3S453_A0A2I3S453_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and sp_Q8MJA0_FOXP2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and sp_P0CF24_FOXP2_RAT_10116 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and sp_Q8MJ97_FOXP2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_F7IF16_F7IF16_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_G1L725_G1L725_AILME_9646 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_G7P2I0_G7P2I0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_A0A2K6CDJ6_A0A2K6CDJ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_A0A2K5YTV8_A0A2K5YTV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_A0A2R9AFL9_A0A2R9AFL9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and sp_Q8HZ00_FOXP2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL29_G1RL29_NOMLE_61853 and tr_A0A2Y9DXW3_A0A2Y9DXW3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G3I4Q1_G3I4Q1_CRIGR_10029 and tr_A0A3Q0CDE6_A0A3Q0CDE6_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QWG5_G3QWG5_GORGO_9595 and tr_F1PGV1_F1PGV1_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3R1I1_G3R1I1_GORGO_9595 and tr_A0A096NKI7_A0A096NKI7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RJT8_G3RJT8_GORGO_9595 and sp_Q8IVH2_FOXP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJT8_G3RJT8_GORGO_9595 and tr_G7P3W3_G7P3W3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RJT8_G3RJT8_GORGO_9595 and tr_A0A2K5L6M9_A0A2K5L6M9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RJT8_G3RJT8_GORGO_9595 and tr_A0A2R9C2Q7_A0A2R9C2Q7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8SWE9_A0A2J8SWE9_PONAB_9601 and sp_Q9H334_FOXP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8SWE9_A0A2J8SWE9_PONAB_9601 and tr_A0A0D9RGN9_A0A0D9RGN9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8SWE9_A0A2J8SWE9_PONAB_9601 and tr_A0A2K5P0G5_A0A2K5P0G5_CERAT_9531 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_W5QGR2_W5QGR2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_G1L176_G1L176_AILME_9646 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_A0A2I2UU10_A0A2I2UU10_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_A0A2U3WDT2_A0A2U3WDT2_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_A0A2U3YGZ0_A0A2U3YGZ0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2R0F1_E2R0F1_CANLF_9615 and tr_A0A384CSW5_A0A384CSW5_URSMA_29073 are exactly identical! WARNING: Sequences tr_K7B8H1_K7B8H1_PANTR_9598 and tr_A0A0D9RFT0_A0A0D9RFT0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_W5PIX5_W5PIX5_SHEEP_9940 and sp_A4IFD2_FOXP1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4ARK3_M4ARK3_XIPMA_8083 and tr_A0A087Y9G6_A0A087Y9G6_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3J7V1_I3J7V1_ORENI_8128 and tr_G3NWU7_G3NWU7_GASAC_69293 are exactly identical! WARNING: Sequences tr_I3J7V1_I3J7V1_ORENI_8128 and tr_A0A2U9BFQ5_A0A2U9BFQ5_SCOMX_52904 are exactly identical! WARNING: Sequences tr_I3MGK6_I3MGK6_ICTTR_43179 and tr_A0A286XI73_A0A286XI73_CAVPO_10141 are exactly identical! WARNING: Sequences tr_I3MGK6_I3MGK6_ICTTR_43179 and tr_A0A1U7UKN0_A0A1U7UKN0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_I3MXT8_I3MXT8_ICTTR_43179 and tr_A0A2R8MRM9_A0A2R8MRM9_CALJA_9483 are exactly identical! WARNING: Sequences tr_I3MXT8_I3MXT8_ICTTR_43179 and tr_A0A287AFQ6_A0A287AFQ6_PIG_9823 are exactly identical! WARNING: Sequences tr_I3MXT8_I3MXT8_ICTTR_43179 and tr_A0A2Y9R498_A0A2Y9R498_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0WLJ9_H0WLJ9_OTOGA_30611 and tr_A0A2K5NW14_A0A2K5NW14_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EXX8_F7EXX8_MACMU_9544 and tr_A0A096NT27_A0A096NT27_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EXX8_F7EXX8_MACMU_9544 and tr_A0A2K5P808_A0A2K5P808_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EXX8_F7EXX8_MACMU_9544 and tr_A0A2K6E3E5_A0A2K6E3E5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FNZ4_F7FNZ4_MACMU_9544 and tr_A0A2K5YV04_A0A2K5YV04_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HDG5_F7HDG5_MACMU_9544 and tr_G1M995_G1M995_AILME_9646 are exactly identical! WARNING: Sequences tr_F7HDG5_F7HDG5_MACMU_9544 and tr_G7NYY4_G7NYY4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HDG5_F7HDG5_MACMU_9544 and tr_A0A384D2Z3_A0A384D2Z3_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7NR98_G7NR98_MACMU_9544 and tr_G7Q2Q5_G7Q2Q5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NR98_G7NR98_MACMU_9544 and tr_A0A2I3MXA5_A0A2I3MXA5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NR98_G7NR98_MACMU_9544 and tr_A0A2K5KQ14_A0A2K5KQ14_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NR98_G7NR98_MACMU_9544 and tr_A0A2K6CM10_A0A2K6CM10_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZI17_H0ZI17_TAEGU_59729 and tr_U3KG46_U3KG46_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZI17_H0ZI17_TAEGU_59729 and tr_U3IWE7_U3IWE7_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0ZI17_H0ZI17_TAEGU_59729 and tr_A0A091VIP6_A0A091VIP6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZSD2_H0ZSD2_TAEGU_59729 and tr_U3JXQ3_U3JXQ3_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZSD2_H0ZSD2_TAEGU_59729 and tr_A0A091EQ73_A0A091EQ73_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZSD2_H0ZSD2_TAEGU_59729 and tr_A0A218ULV3_A0A218ULV3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A337S8C2_A0A337S8C2_FELCA_9685 and tr_A0A2U3W8K6_A0A2U3W8K6_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337S8C2_A0A337S8C2_FELCA_9685 and tr_A0A2Y9J0T7_A0A2Y9J0T7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_R0LLC8_R0LLC8_ANAPL_8839 and tr_A0A093PZ26_A0A093PZ26_9PASS_328815 are exactly identical! WARNING: Sequences tr_R0LLC8_R0LLC8_ANAPL_8839 and tr_A0A091IDB7_A0A091IDB7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A3B1IJC1_A0A3B1IJC1_ASTMX_7994 and tr_W5UEL8_W5UEL8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A015IZN1_A0A015IZN1_9GLOM_1432141 and tr_A0A2H5RAJ0_A0A2H5RAJ0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0F4GSS2_A0A0F4GSS2_9PEZI_1047168 and tr_A0A1X7RUW1_A0A1X7RUW1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_A0A0F8UIY7_A0A0F8UIY7_9EURO_308745 and tr_A0A2T5LYJ3_A0A2T5LYJ3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0F8XT95_A0A0F8XT95_9EURO_308745 and tr_A0A2T5LN56_A0A2T5LN56_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0K0FH81_A0A0K0FH81_STRVS_75913 and tr_A0A0N5C3S6_A0A0N5C3S6_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0A1P7W3_A0A0A1P7W3_9FUNG_58291 and tr_A0A367IZL8_A0A367IZL8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1PB26_A0A0A1PB26_9FUNG_58291 and tr_A0A367J4Z7_A0A367J4Z7_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091EYS4_A0A091EYS4_CORBR_85066 and tr_A0A091FMZ2_A0A091FMZ2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091F4Y9_A0A091F4Y9_CORBR_85066 and tr_A0A091J5F0_A0A091J5F0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F4Y9_A0A091F4Y9_CORBR_85066 and tr_A0A091UP03_A0A091UP03_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F4Y9_A0A091F4Y9_CORBR_85066 and tr_A0A087R2I6_A0A087R2I6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F4Y9_A0A091F4Y9_CORBR_85066 and tr_A0A091XP08_A0A091XP08_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F4Y9_A0A091F4Y9_CORBR_85066 and tr_A0A0A0A1C1_A0A0A0A1C1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JMJ2_A0A091JMJ2_EGRGA_188379 and tr_A0A091WA66_A0A091WA66_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091USI2_A0A091USI2_NIPNI_128390 and tr_A0A087QY64_A0A087QY64_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091GUS6_A0A091GUS6_9AVES_55661 and tr_A0A1V4KAN4_A0A1V4KAN4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CXV3_A0A0V1CXV3_TRIBR_45882 and tr_A0A0V0U5G1_A0A0V0U5G1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WZ34_A0A0V0WZ34_9BILA_92179 and tr_A0A0V1LSC6_A0A0V1LSC6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1Z5SSK3_A0A1Z5SSK3_HORWE_1157616 and tr_A0A1Z5TCQ8_A0A1Z5TCQ8_HORWE_1157616 are exactly identical! WARNING: Sequences tr_A0A226NF86_A0A226NF86_CALSU_9009 and tr_A0A226PPX5_A0A226PPX5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2A2K600_A0A2A2K600_9BILA_2018661 and tr_A0A2A2KPG2_A0A2A2KPG2_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2D0PHJ9_A0A2D0PHJ9_ICTPU_7998 and tr_A0A2D0PKC6_A0A2D0PKC6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RXA0_A0A2D0RXA0_ICTPU_7998 and tr_A0A2D0RY67_A0A2D0RY67_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RXA0_A0A2D0RXA0_ICTPU_7998 and tr_A0A2D0RY72_A0A2D0RY72_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SI59_A0A2D0SI59_ICTPU_7998 and tr_A0A2D0SI60_A0A2D0SI60_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L3E2_A0A2K5L3E2_CERAT_9531 and tr_A0A2K6D0W0_A0A2K6D0W0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5L3E2_A0A2K5L3E2_CERAT_9531 and tr_A0A2K5XRU4_A0A2K5XRU4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3UZH3_A0A2U3UZH3_TURTR_9739 and tr_A0A2Y9NUL6_A0A2Y9NUL6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3UZH3_A0A2U3UZH3_TURTR_9739 and tr_A0A2Y9EWE6_A0A2Y9EWE6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AI81_A0A2U4AI81_TURTR_9739 and tr_A0A2Y9P5C2_A0A2Y9P5C2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BK07_A0A2U4BK07_TURTR_9739 and tr_A0A2Y9NA49_A0A2Y9NA49_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BK07_A0A2U4BK07_TURTR_9739 and tr_A0A2Y9SUC6_A0A2Y9SUC6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BK07_A0A2U4BK07_TURTR_9739 and tr_A0A383YPB9_A0A383YPB9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CCF4_A0A2U4CCF4_TURTR_9739 and tr_A0A2Y9NG51_A0A2Y9NG51_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CCF4_A0A2U4CCF4_TURTR_9739 and tr_A0A384AYX5_A0A384AYX5_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3WID3_A0A2U3WID3_ODORO_9708 and tr_A0A2U3XE47_A0A2U3XE47_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9PHR4_A0A2Y9PHR4_DELLE_9749 and tr_A0A2Y9SH56_A0A2Y9SH56_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 152 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/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.raxml.reduced.phy Alignment comprises 1 partitions and 431 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 431 Gaps: 46.33 % Invariant sites: 0.23 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.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/Q9BZS1/3_mltree/Q9BZS1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 108 / 8640 [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: -173033.904534 [00:00:00 -173033.904534] Initial branch length optimization [00:00:01 -105572.572769] Model parameter optimization (eps = 0.100000) [00:01:04] Tree #1, final logLikelihood: -105387.330074 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.108888,0.098195) (0.070639,0.139308) (0.425066,0.685288) (0.395407,1.740421) 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/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BZS1/4_raxmlng_ancestral/Q9BZS1.raxml.log Analysis started: 04-Jun-2021 13:34:15 / finished: 04-Jun-2021 13:35:24 Elapsed time: 68.396 seconds