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 02-Jun-2021 14:47:23 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/2_msa/P56693_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/3_mltree/P56693.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/4_raxmlng_ancestral/P56693 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622634443 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/P56693/2_msa/P56693_nogap_msa.fasta [00:00:00] Loaded alignment with 997 taxa and 466 sites WARNING: Sequences tr_F1P1Z5_F1P1Z5_CHICK_9031 and sp_P57074_SOX8_CHICK_9031 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_H0ZJW3_H0ZJW3_TAEGU_59729 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_U3KIZ4_U3KIZ4_FICAL_59894 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A091EYU2_A0A091EYU2_CORBR_85066 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A093PXB6_A0A093PXB6_9PASS_328815 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A093HWE3_A0A093HWE3_STRCA_441894 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A0A0A2A4_A0A0A0A2A4_CHAVO_50402 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A091HZF1_A0A091HZF1_CALAN_9244 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A226MZU5_A0A226MZU5_CALSU_9009 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_A0A226PSS4_A0A226PSS4_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q9W7R5_SOX21_CHICK_9031 and tr_A0A226M6J9_A0A226M6J9_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q9W7R5_SOX21_CHICK_9031 and tr_A0A226NYS8_A0A226NYS8_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A226NCN2_A0A226NCN2_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A226PUW5_A0A226PUW5_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_B7SZV3_B7SZV3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A287D385_A0A287D385_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_H0WE30_H0WE30_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2R8P701_A0A2R8P701_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_L5KZV5_L5KZV5_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A1U7QSF6_A0A1U7QSF6_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YGH2_M3YGH2_MUSPF_9669 and tr_A0A2Y9KDX5_A0A2Y9KDX5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YNM2_M3YNM2_MUSPF_9669 and tr_M3VZ63_M3VZ63_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_G1SBJ0_G1SBJ0_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_G3RDD2_G3RDD2_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_G1TJ86_G1TJ86_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2I3TV57_A0A2I3TV57_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_W5Q1Z3_W5Q1Z3_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and sp_O95416_SOX14_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_F7HQE3_F7HQE3_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_G7P040_G7P040_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2I2U9L9_A0A2I2U9L9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A096MSU2_A0A096MSU2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A0D9SC48_A0A0D9SC48_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2K5KS53_A0A2K5KS53_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2K6ANL6_A0A2K6ANL6_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2K5XVC7_A0A2K5XVC7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2R8ZCF2_A0A2R8ZCF2_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2U4B8W6_A0A2U4B8W6_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2U3WV20_A0A2U3WV20_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2U3X925_A0A2U3X925_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2Y9KGL2_A0A2Y9KGL2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2Y9NT43_A0A2Y9NT43_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A2Y9FBD0_A0A2Y9FBD0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A384DHB9_A0A384DHB9_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z4N2_M3Z4N2_MUSPF_9669 and tr_A0A383Z5H6_A0A383Z5H6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_G3RLX8_G3RLX8_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_H2NUK1_H2NUK1_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_H2QDR6_H2QDR6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and sp_P48436_SOX9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_F6PPG2_F6PPG2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and sp_P61753_SOX9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and sp_Q9BG91_SOX9_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_A0A096NU47_A0A096NU47_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_A0A0D9QWJ2_A0A0D9QWJ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_A0A2K5N5T1_A0A2K5N5T1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G6W7_A0A2I3G6W7_NOMLE_61853 and tr_A0A2K6DT16_A0A2K6DT16_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_H2PC44_H2PC44_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_E2R1W3_E2R1W3_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_H2R486_H2R486_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and sp_P54231_SOX2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_H0Y203_H0Y203_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_B8XIA2_B8XIA2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A2VDX8_A2VDX8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_D3U659_D3U659_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A096NUA5_A0A096NUA5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A0D9SC13_A0A0D9SC13_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A1S3GJU6_A0A1S3GJU6_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2K5KW19_A0A2K5KW19_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2K6B307_A0A2K6B307_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2U3X3J9_A0A2U3X3J9_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2U3XIJ2_A0A2U3XIJ2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2Y9JY45_A0A2Y9JY45_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2Y9N1T3_A0A2Y9N1T3_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1SBA9_G1SBA9_NOMLE_61853 and tr_A0A2Y9FML7_A0A2Y9FML7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_H2NK54_H2NK54_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_H0XS41_H0XS41_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and sp_Q9Y651_SOX21_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A1D5Q2F1_A0A1D5Q2F1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A2R8M5Q0_A0A2R8M5Q0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_F2Z520_F2Z520_PIG_9823 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A337SPQ4_A0A337SPQ4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A0D9SA80_A0A0D9SA80_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A2K5KLQ7_A0A2K5KLQ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A2U3WIY9_A0A2U3WIY9_ODORO_9708 are exactly identical! WARNING: Sequences tr_G3RV32_G3RV32_GORGO_9595 and tr_A0A2Y9JDE3_A0A2Y9JDE3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2J8KPH4_A0A2J8KPH4_PANTR_9598 and sp_O60248_SOX15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8LNY1_A0A2J8LNY1_PANTR_9598 and tr_A0A2R9A0H5_A0A2R9A0H5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QKU0_H2QKU0_PANTR_9598 and sp_P35713_SOX18_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and sp_Q06945_SOX4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and tr_F7BAX2_F7BAX2_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and tr_A0A0D9SCM6_A0A0D9SCM6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and tr_A0A2K5KSW9_A0A2K5KSW9_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and tr_A0A2K6AYT6_A0A2K6AYT6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XNT3_F6XNT3_MONDO_13616 and tr_G3WHS5_G3WHS5_SARHA_9305 are exactly identical! WARNING: Sequences tr_D4A543_D4A543_RAT_10116 and tr_A0A1U7QKX9_A0A1U7QKX9_MESAU_10036 are exactly identical! WARNING: Sequences tr_M4AYL9_M4AYL9_XIPMA_8083 and tr_A0A087YS71_A0A087YS71_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AYX6_M4AYX6_XIPMA_8083 and tr_A0A087YSU3_A0A087YSU3_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4B0D0_M4B0D0_XIPMA_8083 and tr_A0A087YRN8_A0A087YRN8_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NK15_A0A158NK15_ATTCE_12957 and tr_A0A195BW04_A0A195BW04_9HYME_520822 are exactly identical! WARNING: Sequences tr_Q6WNT8_Q6WNT8_TAKRU_31033 and tr_Q4SV91_Q4SV91_TETNG_99883 are exactly identical! WARNING: Sequences tr_H3CWK9_H3CWK9_TETNG_99883 and sp_Q6IZ48_SOX8_TETNG_99883 are exactly identical! WARNING: Sequences tr_G3SSE7_G3SSE7_LOXAF_9785 and tr_A0A2Y9DUM9_A0A2Y9DUM9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_U3KIG3_U3KIG3_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_U3HYI1_U3HYI1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A0Q3PLH6_A0A0Q3PLH6_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A093Q8L4_A0A093Q8L4_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A093J9H0_A0A093J9H0_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A091XRL3_A0A091XRL3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A0A0AMQ0_A0A0A0AMQ0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A093GCB4_A0A093GCB4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A091HR26_A0A091HR26_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0Z8W5_H0Z8W5_TAEGU_59729 and tr_A0A1V4KQX0_A0A1V4KQX0_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0ZA76_H0ZA76_TAEGU_59729 and tr_A0A218US57_A0A218US57_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A286ZW65_A0A286ZW65_PIG_9823 and sp_A5A763_SOX10_PIG_9823 are exactly identical! WARNING: Sequences tr_I3LK63_I3LK63_PIG_9823 and tr_A0A337RVV8_A0A337RVV8_FELCA_9685 are exactly identical! WARNING: Sequences tr_I3LK63_I3LK63_PIG_9823 and tr_A0A2U3VEI1_A0A2U3VEI1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337STZ2_A0A337STZ2_FELCA_9685 and tr_A0A2U3WW80_A0A2U3WW80_ODORO_9708 are exactly identical! WARNING: Sequences tr_R0KWE0_R0KWE0_ANAPL_8839 and tr_A0A087RJ12_A0A087RJ12_APTFO_9233 are exactly identical! WARNING: Sequences tr_R0KWE0_R0KWE0_ANAPL_8839 and tr_A0A093GRJ8_A0A093GRJ8_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2K6VYH7_A0A2K6VYH7_ONCVO_6282 and tr_A0A182ELX6_A0A182ELX6_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096MV92_A0A096MV92_PAPAN_9555 and tr_A0A2K5LZ51_A0A2K5LZ51_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MV92_A0A096MV92_PAPAN_9555 and tr_A0A2K6CCT3_A0A2K6CCT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N4N0_A0A096N4N0_PAPAN_9555 and tr_A0A2K5L3D6_A0A2K5L3D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4N0_A0A096N4N0_PAPAN_9555 and tr_A0A2K6ATW4_A0A2K6ATW4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NK02_A0A096NK02_PAPAN_9555 and tr_A0A2K5L248_A0A2K5L248_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RG54_A0A0D9RG54_CHLSB_60711 and tr_A0A2K5NCK4_A0A2K5NCK4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RG54_A0A0D9RG54_CHLSB_60711 and tr_A0A2K6D1T5_A0A2K6D1T5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9RG54_A0A0D9RG54_CHLSB_60711 and tr_A0A2K6A9Y5_A0A2K6A9Y5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0FLP3_A0A0K0FLP3_STRVS_75913 and tr_A0A0N5CDG2_A0A0N5CDG2_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151NGX8_A0A151NGX8_ALLMI_8496 and tr_A0A1U7RC23_A0A1U7RC23_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NHP7_A0A151NHP7_ALLMI_8496 and tr_A0A1U7RMD3_A0A1U7RMD3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_Q9YGP7_Q9YGP7_ALLMI_8496 and tr_A0A1U7SCS0_A0A1U7SCS0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_R7VQH0_R7VQH0_COLLI_8932 and tr_A0A1V4JAX1_A0A1V4JAX1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3KK65_A0A1S3KK65_SALSA_8030 and tr_A0A060Y4B1_A0A060Y4B1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PMG1_A0A1S3PMG1_SALSA_8030 and tr_A0A060WTL2_A0A060WTL2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3RTX5_A0A1S3RTX5_SALSA_8030 and tr_A0A060WMX3_A0A060WMX3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MZW2_A0A226MZW2_CALSU_9009 and tr_A0A226PCU3_A0A226PCU3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NN65_A0A226NN65_CALSU_9009 and tr_A0A226PPA0_A0A226PPA0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3VAD4_A0A2U3VAD4_TURTR_9739 and tr_A0A2Y9T670_A0A2Y9T670_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4A6V4_A0A2U4A6V4_TURTR_9739 and tr_A0A2Y9NI67_A0A2Y9NI67_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A6V4_A0A2U4A6V4_TURTR_9739 and tr_A0A2Y9STB0_A0A2Y9STB0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AJ34_A0A2U4AJ34_TURTR_9739 and tr_A0A2Y9M570_A0A2Y9M570_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C5Q8_A0A2U4C5Q8_TURTR_9739 and tr_A0A2Y9SQ96_A0A2Y9SQ96_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3WP77_A0A2U3WP77_ODORO_9708 and tr_A0A2U3YWQ9_A0A2U3YWQ9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9QB75_A0A2Y9QB75_DELLE_9749 and tr_A0A2Y9EYU4_A0A2Y9EYU4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9QB75_A0A2Y9QB75_DELLE_9749 and tr_A0A384AP26_A0A384AP26_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 146 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/P56693/4_raxmlng_ancestral/P56693.raxml.reduced.phy Alignment comprises 1 partitions and 466 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 466 Gaps: 42.61 % Invariant sites: 0.43 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/4_raxmlng_ancestral/P56693.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/P56693/3_mltree/P56693.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 117 / 9360 [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: -270103.042636 [00:00:00 -270103.042636] Initial branch length optimization [00:00:02 -140205.901050] Model parameter optimization (eps = 0.100000) [00:02:13] Tree #1, final logLikelihood: -140057.457213 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.085237,0.069653) (0.080386,0.289018) (0.239864,0.582123) (0.594514,1.398117) 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/P56693/4_raxmlng_ancestral/P56693.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/4_raxmlng_ancestral/P56693.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/4_raxmlng_ancestral/P56693.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P56693/4_raxmlng_ancestral/P56693.raxml.log Analysis started: 02-Jun-2021 14:47:23 / finished: 02-Jun-2021 14:49:44 Elapsed time: 141.544 seconds