RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 18:00:53 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/2_msa/P35716_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/3_mltree/P35716.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102053 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/2_msa/P35716_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 441 sites WARNING: Sequences tr_B4QJY2_B4QJY2_DROSI_7240 and tr_B4HHC6_B4HHC6_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QJY4_B4QJY4_DROSI_7240 and sp_Q24533_DICH_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QJY4_B4QJY4_DROSI_7240 and tr_B4HHC8_B4HHC8_DROSE_7238 are exactly identical! WARNING: Sequences sp_P48430_SOX2_CHICK_9031 and tr_K7EXN5_K7EXN5_PELSI_13735 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_A0A226NYS8_A0A226NYS8_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_H0Z8W5_H0Z8W5_TAEGU_59729 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_U3KIG3_U3KIG3_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_U3HYI1_U3HYI1_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A151NGX8_A0A151NGX8_ALLMI_8496 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A0Q3PLH6_A0A0Q3PLH6_AMAAE_12930 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093Q8L4_A0A093Q8L4_9PASS_328815 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A091UW48_A0A091UW48_NIPNI_128390 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093J9H0_A0A093J9H0_STRCA_441894 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A091XRL3_A0A091XRL3_OPIHO_30419 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A0A0AMQ0_A0A0A0AMQ0_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093GCB4_A0A093GCB4_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A091HR26_A0A091HR26_CALAN_9244 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A1U7RC23_A0A1U7RC23_ALLSI_38654 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A1V4KQX0_A0A1V4KQX0_PATFA_372326 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_M3Z4N2_M3Z4N2_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G1SBJ0_G1SBJ0_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G3RDD2_G3RDD2_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G1TJ86_G1TJ86_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2I3TV57_A0A2I3TV57_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_W5Q1Z3_W5Q1Z3_SHEEP_9940 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 sp_O95416_SOX14_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_F7HQE3_F7HQE3_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G5BC40_G5BC40_HETGA_10181 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_G7P040_G7P040_MACFA_9541 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_A0A2I2U9L9_A0A2I2U9L9_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A096MSU2_A0A096MSU2_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A091EBT3_A0A091EBT3_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A0D9SC48_A0A0D9SC48_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A1U7QSF6_A0A1U7QSF6_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K5KS53_A0A2K5KS53_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K6ANL6_A0A2K6ANL6_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K5XVC7_A0A2K5XVC7_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2R8ZCF2_A0A2R8ZCF2_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U4B8W6_A0A2U4B8W6_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U3WV20_A0A2U3WV20_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U3X925_A0A2U3X925_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9KGL2_A0A2Y9KGL2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9NT43_A0A2Y9NT43_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9FBD0_A0A2Y9FBD0_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A384DHB9_A0A384DHB9_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A383Z5H6_A0A383Z5H6_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_G3RV32_G3RV32_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_H2NK54_H2NK54_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and sp_Q9Y651_SOX21_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A1D5Q2F1_A0A1D5Q2F1_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2R8M5Q0_A0A2R8M5Q0_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_F2Z520_F2Z520_PIG_9823 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A337SPQ4_A0A337SPQ4_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A0D9SA80_A0A0D9SA80_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2K5KLQ7_A0A2K5KLQ7_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2K6ARY4_A0A2K6ARY4_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2U4A6V4_A0A2U4A6V4_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2U3WIY9_A0A2U3WIY9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2Y9JDE3_A0A2Y9JDE3_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2Y9NI67_A0A2Y9NI67_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q811W0_SOX21_MOUSE_10090 and tr_A0A2Y9STB0_A0A2Y9STB0_PHYCD_9755 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_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 sp_P48431_SOX2_HUMAN_9606 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_B1PXF9_B1PXF9_PIG_9823 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_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_A0A2Y9FML7_A0A2Y9FML7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and sp_P35716_SOX11_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QS49_G3QS49_GORGO_9595 and sp_Q9BT81_SOX7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q290B8_Q290B8_DROPS_46245 and tr_B4GCG7_B4GCG7_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2R1W3_E2R1W3_CANLF_9615 and tr_A0A2Y9N1T3_A0A2Y9N1T3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2J8KPH4_A0A2J8KPH4_PANTR_9598 and sp_O60248_SOX15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R7L3_H2R7L3_PANTR_9598 and sp_Q06945_SOX4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CW19_K7CW19_PANTR_9598 and sp_O15370_SOX12_HUMAN_9606 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_M4AYS5_M4AYS5_XIPMA_8083 and tr_I3KZ58_I3KZ58_ORENI_8128 are exactly identical! WARNING: Sequences tr_M4AYS5_M4AYS5_XIPMA_8083 and tr_A0A087YQH6_A0A087YQH6_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4B0D0_M4B0D0_XIPMA_8083 and tr_A0A087YRN8_A0A087YRN8_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NLR6_A0A158NLR6_ATTCE_12957 and tr_F4X2P5_F4X2P5_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NLW3_A0A158NLW3_ATTCE_12957 and tr_A0A195BK79_A0A195BK79_9HYME_520822 are exactly identical! WARNING: Sequences tr_Q6WNT8_Q6WNT8_TAKRU_31033 and tr_Q4SV91_Q4SV91_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A0H5S245_A0A0H5S245_BRUMA_6279 and tr_A0A1I7VNN3_A0A1I7VNN3_LOALO_7209 are exactly identical! WARNING: Sequences tr_A0A1D5R7Q8_A0A1D5R7Q8_MACMU_9544 and tr_A0A2K5L0J2_A0A2K5L0J2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BAX2_F7BAX2_MACMU_9544 and tr_A0A0D9SCM6_A0A0D9SCM6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BAX2_F7BAX2_MACMU_9544 and tr_A0A2K5KSW9_A0A2K5KSW9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BAX2_F7BAX2_MACMU_9544 and tr_A0A2K6AYT6_A0A2K6AYT6_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SIA6_E5SIA6_TRISP_6334 and tr_A0A0V0XYN1_A0A0V0XYN1_TRIPS_6337 are exactly identical! WARNING: Sequences tr_G3SSE7_G3SSE7_LOXAF_9785 and tr_A0A2Y9DUM9_A0A2Y9DUM9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A337RVV8_A0A337RVV8_FELCA_9685 and tr_A0A2U3VEI1_A0A2U3VEI1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2K6VYH7_A0A2K6VYH7_ONCVO_6282 and tr_A0A182ELX6_A0A182ELX6_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096MZ97_A0A096MZ97_PAPAN_9555 and tr_A0A2K5M610_A0A2K5M610_CERAT_9531 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_A0A151MVN3_A0A151MVN3_ALLMI_8496 and tr_A0A1U7SCR6_A0A1U7SCR6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091K6J2_A0A091K6J2_EGRGA_188379 and tr_A0A087RJ12_A0A087RJ12_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091K6J2_A0A091K6J2_EGRGA_188379 and tr_A0A2I0MBE9_A0A2I0MBE9_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091K6J2_A0A091K6J2_EGRGA_188379 and tr_A0A093GRJ8_A0A093GRJ8_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A093H204_A0A093H204_DRYPU_118200 and tr_A0A1V4KYG0_A0A1V4KYG0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V0WVR9_A0A0V0WVR9_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V0VQ67_A0A0V0VQ67_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V1LB14_A0A0V1LB14_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V1PCW0_A0A0V1PCW0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V0UCJ5_A0A0V0UCJ5_9BILA_144512 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_A0A1S3RHM6_A0A1S3RHM6_SALSA_8030 and tr_A0A060VUT3_A0A060VUT3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3RTX5_A0A1S3RTX5_SALSA_8030 and tr_A0A060WMX3_A0A060WMX3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7U6X1_A0A1I7U6X1_9PELO_1561998 and tr_A0A1I7U6X2_A0A1I7U6X2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226NDZ2_A0A226NDZ2_CALSU_9009 and tr_A0A226P3V3_A0A226P3V3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2Y9PYS2_A0A2Y9PYS2_DELLE_9749 and tr_A0A2Y9T6H2_A0A2Y9T6H2_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 143 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.reduced.phy Alignment comprises 1 partitions and 441 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 441 Gaps: 53.56 % Invariant sites: 2.72 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/3_mltree/P35716.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 111 / 8880 [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: -207061.293986 [00:00:00 -207061.293986] Initial branch length optimization [00:00:01 -118597.568702] Model parameter optimization (eps = 0.100000) [00:00:39] Tree #1, final logLikelihood: -118342.622279 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.080427,0.051454) (0.080432,0.168978) (0.245434,0.686167) (0.593707,1.370813) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35716/4_raxmlng_ancestral/P35716.raxml.log Analysis started: 12-Jul-2021 18:00:53 / finished: 12-Jul-2021 18:01:37 Elapsed time: 44.084 seconds Consumed energy: 3.921 Wh