RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 02:25:29 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/2_msa/Q13285_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/3_mltree/Q13285.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676329 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/2_msa/Q13285_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 461 sites WARNING: Sequences tr_B4Q4C8_B4Q4C8_DROSI_7240 and sp_Q05192_FTF1B_DROME_7227 are exactly identical! WARNING: Sequences tr_B4Q4C8_B4Q4C8_DROSI_7240 and tr_B4IFM9_B4IFM9_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_G1NJI1_G1NJI1_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_U3JVB1_U3JVB1_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_U3IYD5_U3IYD5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A091F5B7_A0A091F5B7_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A091KF60_A0A091KF60_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A093QCI4_A0A093QCI4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A091W043_A0A091W043_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A087R4X0_A0A087R4X0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A091VDI9_A0A091VDI9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A091GGB5_A0A091GGB5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A0A0ALX1_A0A0A0ALX1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A2I0MPN1_A0A2I0MPN1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5NVI7_A0A1D5NVI7_CHICK_9031 and tr_A0A1V4KFZ7_A0A1V4KFZ7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_G1NAZ5_G1NAZ5_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_G1KEF6_G1KEF6_ANOCA_28377 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_F6R995_F6R995_ORNAN_9258 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_F6QPZ5_F6QPZ5_MONDO_13616 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_K7FDF3_K7FDF3_PELSI_13735 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_G3WA42_G3WA42_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_H0YXC7_H0YXC7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_U3KCN2_U3KCN2_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_U3ICB1_U3ICB1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A0Q3UR70_A0A0Q3UR70_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A091F459_A0A091F459_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A091JRM4_A0A091JRM4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A091VSG6_A0A091VSG6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A087QXC1_A0A087QXC1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A093JHK5_A0A093JHK5_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A091GHM4_A0A091GHM4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A0A0A201_A0A0A0A201_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A2I0M533_A0A2I0M533_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A093GA30_A0A093GA30_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A091ITM6_A0A091ITM6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5PH30_A0A1D5PH30_CHICK_9031 and tr_A0A218V4K8_A0A218V4K8_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NVB5_F1NVB5_CHICK_9031 and tr_G1N2K3_G1N2K3_MELGA_9103 are exactly identical! WARNING: Sequences sp_O08580_ERR1_MOUSE_10090 and tr_G3I885_G3I885_CRIGR_10029 are exactly identical! WARNING: Sequences sp_O08580_ERR1_MOUSE_10090 and sp_Q5QJV7_ERR1_RAT_10116 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_G1RVM3_G1RVM3_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_G3GRF2_G3GRF2_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_H2N3Q0_H2N3Q0_PONAB_9601 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_G1SEH2_G1SEH2_RABIT_9986 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_E2R7U1_E2R7U1_CANLF_9615 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_W5PNX1_W5PNX1_SHEEP_9940 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and sp_P62510_ERR3_RAT_10116 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_I3MDN3_I3MDN3_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_H0XBZ1_H0XBZ1_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A286XP90_A0A286XP90_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and sp_P62508_ERR3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_G3TQM6_G3TQM6_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_F7H9C3_F7H9C3_CALJA_9483 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A287BBC6_A0A287BBC6_PIG_9823 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_E1BC39_E1BC39_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A0D9RT24_A0A0D9RT24_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A1S3A0E3_A0A1S3A0E3_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A1S3F347_A0A1S3F347_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A3Q0EBA6_A0A3Q0EBA6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A1U8CPR2_A0A1U8CPR2_MESAU_10036 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2U3UZV9_A0A2U3UZV9_TURTR_9739 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2U3V0B1_A0A2U3V0B1_TURTR_9739 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2U4A4F3_A0A2U4A4F3_TURTR_9739 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2Y9DJU8_A0A2Y9DJU8_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2Y9NPV9_A0A2Y9NPV9_DELLE_9749 are exactly identical! WARNING: Sequences sp_P62509_ERR3_MOUSE_10090 and tr_A0A2Y9FL95_A0A2Y9FL95_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P20153_USP_DROME_7227 and tr_B4I9M8_B4I9M8_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q8WS79_Q8WS79_DROME_7227 and tr_B4HJD7_B4HJD7_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_G1PCE9_G1PCE9_MYOLU_59463 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_F1PFF7_F1PFF7_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_K7DJ98_K7DJ98_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_I3N8Q2_I3N8Q2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_H0XSB3_H0XSB3_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_F7E0X8_F7E0X8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2R8PCD0_A0A2R8PCD0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_F1RQP2_F1RQP2_PIG_9823 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_G1MHZ6_G1MHZ6_AILME_9646 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_F1MBX3_F1MBX3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_M3X2Z4_M3X2Z4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A0D9R4C8_A0A0D9R4C8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A1S3FJT4_A0A1S3FJT4_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2K5L8D5_A0A2K5L8D5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2K6B4D5_A0A2K6B4D5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2K5Z665_A0A2K5Z665_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2R9BL88_A0A2R9BL88_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2U4B129_A0A2U4B129_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2Y9DZ78_A0A2Y9DZ78_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1QYL6_G1QYL6_NOMLE_61853 and tr_A0A2Y9EII0_A0A2Y9EII0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1S650_G1S650_NOMLE_61853 and tr_H2QXV6_H2QXV6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S650_G1S650_NOMLE_61853 and tr_A0A2R9B1E3_A0A2R9B1E3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1S2ZM55_A0A1S2ZM55_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1U7RBT2_A0A1U7RBT2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2Y1Q8_A0A2I2Y1Q8_GORGO_9595 and tr_A0A2J8PK71_A0A2J8PK71_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y1Q8_A0A2I2Y1Q8_GORGO_9595 and tr_A0A0D9RHQ2_A0A0D9RHQ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Y1Q8_A0A2I2Y1Q8_GORGO_9595 and tr_A0A2K5LLT6_A0A2K5LLT6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Y1Q8_A0A2I2Y1Q8_GORGO_9595 and tr_A0A2R9B8V6_A0A2R9B8V6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2I3T916_A0A2I3T916_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_G1L390_G1L390_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_G7NTZ4_G7NTZ4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2I3LJD1_A0A2I3LJD1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2K5P240_A0A2K5P240_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2K6DWH0_A0A2K6DWH0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2K5ZZV6_A0A2K5ZZV6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2R9B4N7_A0A2R9B4N7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2U3ZS83_A0A2U3ZS83_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I2ZN06_A0A2I2ZN06_GORGO_9595 and tr_A0A2U3XZN9_A0A2U3XZN9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_H2N494_H2N494_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_H2Q0V0_H2Q0V0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_H0XVM2_H0XVM2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and sp_O00482_NR5A2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_G7NWH4_G7NWH4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A2I3N372_A0A2I3N372_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A0D9RMJ9_A0A0D9RMJ9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A2K5P732_A0A2K5P732_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A2K6CHD2_A0A2K6CHD2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A2K6AE70_A0A2K6AE70_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R3Z2_G3R3Z2_GORGO_9595 and tr_A0A2R9BR60_A0A2R9BR60_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8TYL4_A0A2J8TYL4_PONAB_9601 and sp_P11474_ERR1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8TYL4_A0A2J8TYL4_PONAB_9601 and tr_A0A096NQ39_A0A096NQ39_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_F6V776_F6V776_CANLF_9615 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_F7AEP9_F7AEP9_HORSE_9796 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_I3NCG1_I3NCG1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_F7IDY1_F7IDY1_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_A0A287B3Q2_A0A287B3Q2_PIG_9823 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_G7PB19_G7PB19_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_F1N0K9_F1N0K9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2NLV4_H2NLV4_PONAB_9601 and tr_A0A384AB56_A0A384AB56_BALAS_310752 are exactly identical! WARNING: Sequences tr_Q29KM6_Q29KM6_DROPS_46245 and tr_B4GT36_B4GT36_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K5Y2K6_A0A2K5Y2K6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_U3J0G8_U3J0G8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A091JE53_A0A091JE53_EGRGA_188379 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A091UQP9_A0A091UQP9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A087R4Q8_A0A087R4Q8_APTFO_9233 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A093H9R3_A0A093H9R3_STRCA_441894 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A091V921_A0A091V921_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A2I0M3Q9_A0A2I0M3Q9_COLLI_8932 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A091I5Q5_A0A091I5Q5_CALAN_9244 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_A0A1V4J7B0_A0A1V4J7B0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A3B5QIW1_A0A3B5QIW1_XIPMA_8083 and tr_A0A087Y9K1_A0A087Y9K1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5R0L0_A0A3B5R0L0_XIPMA_8083 and tr_A0A087YM74_A0A087YM74_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AT38_M4AT38_XIPMA_8083 and tr_A0A2U9BCS7_A0A2U9BCS7_SCOMX_52904 are exactly identical! WARNING: Sequences tr_A0A158NB71_A0A158NB71_ATTCE_12957 and tr_F4WPH2_F4WPH2_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NB71_A0A158NB71_ATTCE_12957 and tr_A0A151ITL8_A0A151ITL8_9HYME_471704 are exactly identical! WARNING: Sequences tr_I3KWE2_I3KWE2_ORENI_8128 and tr_A0A2I4BJP6_A0A2I4BJP6_9TELE_52670 are exactly identical! WARNING: Sequences tr_F7DBF0_F7DBF0_MACMU_9544 and tr_A0A2I3LDG3_A0A2I3LDG3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DBF0_F7DBF0_MACMU_9544 and tr_A0A2K6CS01_A0A2K6CS01_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DBF0_F7DBF0_MACMU_9544 and tr_A0A2K6A1Z9_A0A2K6A1Z9_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5S322_E5S322_TRISP_6334 and tr_A0A0V1LQC6_A0A0V1LQC6_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5S322_E5S322_TRISP_6334 and tr_A0A0V1A9P1_A0A0V1A9P1_9BILA_990121 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_H0Z1W6_H0Z1W6_TAEGU_59729 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_U3IP55_U3IP55_ANAPL_8839 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_A0A091IYC7_A0A091IYC7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_A0A091VZ21_A0A091VZ21_NIPNI_128390 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_A0A087R9J2_A0A087R9J2_APTFO_9233 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_A0A091W763_A0A091W763_OPIHO_30419 are exactly identical! WARNING: Sequences tr_K7F721_K7F721_PELSI_13735 and tr_A0A0A0AJF5_A0A0A0AJF5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0YPS1_H0YPS1_TAEGU_59729 and tr_A0A091E612_A0A091E612_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A091FAL0_A0A091FAL0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A093Q422_A0A093Q422_9PASS_328815 are exactly identical! WARNING: Sequences tr_F4WPT4_F4WPT4_ACREC_103372 and tr_A0A195EH28_A0A195EH28_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WPT4_F4WPT4_ACREC_103372 and tr_A0A195AX26_A0A195AX26_9HYME_520822 are exactly identical! WARNING: Sequences tr_U3JJ78_U3JJ78_FICAL_59894 and tr_A0A2I0MDY7_A0A2I0MDY7_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3JJ78_U3JJ78_FICAL_59894 and tr_A0A1V4JYJ8_A0A1V4JYJ8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I3LG00_A0A2I3LG00_PAPAN_9555 and tr_A0A0D9RM81_A0A0D9RM81_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3LG00_A0A2I3LG00_PAPAN_9555 and tr_A0A2K5LZ53_A0A2K5LZ53_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LG00_A0A2I3LG00_PAPAN_9555 and tr_A0A2K6CW08_A0A2K6CW08_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LG00_A0A2I3LG00_PAPAN_9555 and tr_A0A2K5YBP6_A0A2K5YBP6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MLD8_A0A151MLD8_ALLMI_8496 and tr_A0A1U7R8I9_A0A1U7R8I9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P3F0_A0A151P3F0_ALLMI_8496 and tr_A0A1U7SET8_A0A1U7SET8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0R3RK47_A0A0R3RK47_9BILA_1147741 and tr_A0A183HYM4_A0A183HYM4_9BILA_387005 are exactly identical! WARNING: Sequences tr_A0A0V1CQE3_A0A0V1CQE3_TRIBR_45882 and tr_A0A0V0VRM1_A0A0V0VRM1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D6Q4_A0A0V1D6Q4_TRIBR_45882 and tr_A0A0V0VI12_A0A0V0VI12_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WT00_A0A0V0WT00_9BILA_92179 and tr_A0A0V1KY79_A0A0V1KY79_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WT00_A0A0V0WT00_9BILA_92179 and tr_A0A0V1A6L7_A0A0V1A6L7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0WT00_A0A0V0WT00_9BILA_92179 and tr_A0A0V0TWY7_A0A0V0TWY7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X7S2_A0A0V0X7S2_9BILA_92179 and tr_A0A0V1KXW4_A0A0V1KXW4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UQX2_A0A0V0UQX2_9BILA_181606 and tr_A0A0V0U5N6_A0A0V0U5N6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MZ05_A0A0V1MZ05_9BILA_268474 and tr_A0A0V1HIE3_A0A0V1HIE3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A151XB37_A0A151XB37_9HYME_64791 and tr_A0A195DHV7_A0A195DHV7_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151XB37_A0A151XB37_9HYME_64791 and tr_A0A195EQJ4_A0A195EQJ4_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3I7W4_A0A1S3I7W4_LINUN_7574 and tr_A0A1S3K479_A0A1S3K479_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3M7J0_A0A1S3M7J0_SALSA_8030 and tr_A0A060W630_A0A060W630_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226N242_A0A226N242_CALSU_9009 and tr_A0A226NQ93_A0A226NQ93_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0R1E0_A0A2D0R1E0_ICTPU_7998 and tr_Q3YPH1_Q3YPH1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQD1_A0A2D0RQD1_ICTPU_7998 and tr_A0A2D0RQD6_A0A2D0RQD6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQD1_A0A2D0RQD1_ICTPU_7998 and tr_A0A2D0RRC7_A0A2D0RRC7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQD1_A0A2D0RQD1_ICTPU_7998 and tr_A0A2D0RRY2_A0A2D0RRY2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3VDT3_A0A2U3VDT3_ODORO_9708 and tr_A0A2U3XE63_A0A2U3XE63_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 187 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.reduced.phy Alignment comprises 1 partitions and 461 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 461 Gaps: 27.19 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/3_mltree/Q13285.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 116 / 9280 [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: -128918.717999 [00:00:00 -128918.717999] Initial branch length optimization [00:00:00 -125780.016057] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -125574.764931 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.123913,0.285737) (0.154417,0.418367) (0.367100,0.803865) (0.354570,1.705986) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13285/4_raxmlng_ancestral/Q13285.raxml.log Analysis started: 03-Jun-2021 02:25:29 / finished: 03-Jun-2021 02:26:12 Elapsed time: 42.724 seconds Consumed energy: 3.338 Wh