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 18:10:57 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/2_msa/Q8N7X1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/3_mltree/Q8N7X1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/4_raxmlng_ancestral/Q8N7X1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102657 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/Q8N7X1/2_msa/Q8N7X1_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 1067 sites WARNING: Sequences tr_F1NZD3_F1NZD3_CHICK_9031 and tr_G1MWZ1_G1MWZ1_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NZD3_F1NZD3_CHICK_9031 and tr_U3IUN7_U3IUN7_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NZD3_F1NZD3_CHICK_9031 and tr_A0A226NJ27_A0A226NJ27_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NZD3_F1NZD3_CHICK_9031 and tr_A0A226PHC1_A0A226PHC1_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q5ZLU8_Q5ZLU8_CHICK_9031 and tr_A0A226MHE9_A0A226MHE9_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q5ZLU8_Q5ZLU8_CHICK_9031 and tr_A0A226PEN7_A0A226PEN7_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q9DDU8_Q9DDU8_CHICK_9031 and tr_G1MV83_G1MV83_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q9DDU8_Q9DDU8_CHICK_9031 and tr_U3KFX7_U3KFX7_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q9DDU8_Q9DDU8_CHICK_9031 and tr_U3I859_U3I859_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q9DDU8_Q9DDU8_CHICK_9031 and tr_A0A0Q3P7V5_A0A0Q3P7V5_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q9DDU8_Q9DDU8_CHICK_9031 and tr_A0A218UF36_A0A218UF36_9PASE_299123 are exactly identical! WARNING: Sequences sp_P60824_CIRBP_MOUSE_10090 and tr_G3HF68_G3HF68_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P60824_CIRBP_MOUSE_10090 and sp_P60825_CIRBP_RAT_10116 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_M3XVM4_M3XVM4_MUSPF_9669 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2I3G2U7_A0A2I3G2U7_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_G1P5J2_G1P5J2_MYOLU_59463 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_G3HKN2_G3HKN2_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_G3R305_G3R305_GORGO_9595 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_H2PC92_H2PC92_PONAB_9601 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_G1U9B4_G1U9B4_RABIT_9986 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_H2QNW6_H2QNW6_PANTR_9598 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_F7DAK4_F7DAK4_ORNAN_9258 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_F7DUM8_F7DUM8_MONDO_13616 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and sp_P62997_TRA2B_RAT_10116 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_I3M8E8_I3M8E8_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and sp_P62995_TRA2B_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_F6TT71_F6TT71_MACMU_9544 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_F6ZDN6_F6ZDN6_CALJA_9483 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_Q06AA7_Q06AA7_PIG_9823 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and sp_Q3ZBT6_TRA2B_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_M3WDF5_M3WDF5_FELCA_9685 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A096N3T3_A0A096N3T3_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A0D9RNI1_A0A0D9RNI1_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A1S2ZID6_A0A1S2ZID6_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A1S3GN52_A0A1S3GN52_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A1U7TFX3_A0A1U7TFX3_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A3Q0CUI3_A0A3Q0CUI3_MESAU_10036 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2K5NAJ1_A0A2K5NAJ1_CERAT_9531 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2K6CBA7_A0A2K6CBA7_MACNE_9545 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2K5XDL8_A0A2K5XDL8_MANLE_9568 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2R9B6E8_A0A2R9B6E8_PANPA_9597 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2U3XPQ3_A0A2U3XPQ3_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2Y9DWF7_A0A2Y9DWF7_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2Y9JF85_A0A2Y9JF85_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2Y9MUB2_A0A2Y9MUB2_DELLE_9749 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A2Y9FJP4_A0A2Y9FJP4_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A384D8R6_A0A384D8R6_URSMA_29073 are exactly identical! WARNING: Sequences sp_P62996_TRA2B_MOUSE_10090 and tr_A0A384B7R9_A0A384B7R9_BALAS_310752 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_H2PWY1_H2PWY1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_E2R068_E2R068_CANLF_9615 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and sp_A5A6M3_RBMX_PANTR_9598 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_F6XJB9_F6XJB9_HORSE_9796 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and sp_P38159_RBMX_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_M3W2U4_M3W2U4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_A0A2R8ZZJ3_A0A2R8ZZJ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_A0A2U3ZRV1_A0A2U3ZRV1_ODORO_9708 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_A0A2U3YND3_A0A2U3YND3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_A0A2Y9IF74_A0A2Y9IF74_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G9KKJ5_G9KKJ5_MUSPF_9669 and tr_A0A2Y9LXM0_A0A2Y9LXM0_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_F6XHA7_F6XHA7_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_L5L6N6_L5L6N6_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_A0A1S3FPN1_A0A1S3FPN1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_A0A2U3ZAS2_A0A2U3ZAS2_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_A0A2U3YAU6_A0A2U3YAU6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1QFE5_G1QFE5_MYOLU_59463 and tr_A0A384DRM5_A0A384DRM5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3H9H7_G3H9H7_CRIGR_10029 and tr_A0A1U7QNT2_A0A1U7QNT2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A0E1S0P5_A0A0E1S0P5_COCIM_246410 and tr_E9DI03_E9DI03_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1S0P5_A0A0E1S0P5_COCIM_246410 and tr_A0A0J6YEG2_A0A0J6YEG2_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QVN3_B6QVN3_TALMQ_441960 and tr_A0A093VTU1_A0A093VTU1_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and sp_Q5RF83_CIRBP_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and sp_Q14011_CIRBP_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_F7DU86_F7DU86_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_G7PYA6_G7PYA6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_A0A2I3LFF5_A0A2I3LFF5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_A0A0D9RIJ2_A0A0D9RIJ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_A0A2K6C4I3_A0A2K6C4I3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QIT4_G3QIT4_GORGO_9595 and tr_A0A2R9B0C3_A0A2R9B0C3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A2J8R8N0_A0A2J8R8N0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_H2QYJ9_H2QYJ9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and sp_P98179_RBM3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A2I3MGL6_A0A2I3MGL6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A0D9RLC1_A0A0D9RLC1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A2K6DQM1_A0A2K6DQM1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A2K6A584_A0A2K6A584_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QST9_G3QST9_GORGO_9595 and tr_A0A2R9AXF1_A0A2R9AXF1_PANPA_9597 are exactly identical! WARNING: Sequences tr_C0NAS6_C0NAS6_AJECG_447093 and tr_F0UJD1_F0UJD1_AJEC8_544711 are exactly identical! WARNING: Sequences tr_B8N8I7_B8N8I7_ASPFN_332952 and tr_Q2UHP2_Q2UHP2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_E2RD37_E2RD37_CANLF_9615 and tr_H0WRY6_H0WRY6_OTOGA_30611 are exactly identical! WARNING: Sequences tr_E2RD37_E2RD37_CANLF_9615 and tr_G5BT96_G5BT96_HETGA_10181 are exactly identical! WARNING: Sequences tr_E2RD37_E2RD37_CANLF_9615 and tr_G7NYM6_G7NYM6_MACFA_9541 are exactly identical! WARNING: Sequences tr_E2RD37_E2RD37_CANLF_9615 and tr_A0A2U3WVE3_A0A2U3WVE3_ODORO_9708 are exactly identical! WARNING: Sequences tr_W5PP54_W5PP54_SHEEP_9940 and tr_Q3SZN4_Q3SZN4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FIY0_F9FIY0_FUSOF_660025 and tr_X0C222_X0C222_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FIY0_F9FIY0_FUSOF_660025 and tr_A0A2H3U5F2_A0A2H3U5F2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_H0VKT5_H0VKT5_CAVPO_10141 and tr_D3JUI8_D3JUI8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H0VKT5_H0VKT5_CAVPO_10141 and tr_A0A091DYV3_A0A091DYV3_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A0E0J916_A0A0E0J916_ORYNI_4536 and tr_I1R848_I1R848_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0J916_A0A0E0J916_ORYNI_4536 and tr_A0A0D3HX19_A0A0D3HX19_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_F4P9N8_F4P9N8_BATDJ_684364 and tr_A0A177WW97_A0A177WW97_BATDE_403673 are exactly identical! WARNING: Sequences tr_K7FX00_K7FX00_PELSI_13735 and tr_A0A151N851_A0A151N851_ALLMI_8496 are exactly identical! WARNING: Sequences tr_K7FX00_K7FX00_PELSI_13735 and tr_A0A1U7S6L7_A0A1U7S6L7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_I1PEE9_I1PEE9_ORYGL_4538 and tr_A0A0E0NZL5_A0A0E0NZL5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1PEE9_I1PEE9_ORYGL_4538 and tr_Q7Y008_Q7Y008_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1Q8N0_I1Q8N0_ORYGL_4538 and tr_A0A0D3GN53_A0A0D3GN53_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1Q8N0_I1Q8N0_ORYGL_4538 and tr_A0A0E0AGP3_A0A0E0AGP3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1QTD2_I1QTD2_ORYGL_4538 and tr_A0A0E0QXH8_A0A0E0QXH8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1QTD2_I1QTD2_ORYGL_4538 and tr_A0A0D3HC77_A0A0D3HC77_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1QTD2_I1QTD2_ORYGL_4538 and tr_A0A0E0B8Y2_A0A0E0B8Y2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G3SWH5_G3SWH5_LOXAF_9785 and tr_A0A2Y9FY41_A0A2Y9FY41_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YRK3_H0YRK3_TAEGU_59729 and tr_A0A091FU46_A0A091FU46_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YRK3_H0YRK3_TAEGU_59729 and tr_A0A218U9J0_A0A218U9J0_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z8P1_H0Z8P1_TAEGU_59729 and tr_A0A091F372_A0A091F372_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z8P1_H0Z8P1_TAEGU_59729 and tr_A0A093PT69_A0A093PT69_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z8P1_H0Z8P1_TAEGU_59729 and tr_A0A091FLX6_A0A091FLX6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0E0NZC7_A0A0E0NZC7_ORYRU_4529 and tr_Q10FE7_Q10FE7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0RHL4_A0A0E0RHL4_ORYRU_4529 and tr_Q2QQ97_Q2QQ97_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0RKD9_A0A0E0RKD9_ORYRU_4529 and tr_Q2QLR2_Q2QLR2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F2SP44_F2SP44_TRIRC_559305 and tr_A0A178F3K7_A0A178F3K7_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RIY8_B3RIY8_TRIAD_10228 and tr_A0A369RY94_A0A369RY94_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A0D2Y0I9_A0A0D2Y0I9_FUSO4_426428 and tr_N4TUN0_N4TUN0_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_L5JVH8_L5JVH8_PTEAL_9402 and tr_A0A2U3VNY4_A0A2U3VNY4_ODORO_9708 are exactly identical! WARNING: Sequences tr_L5JVH8_L5JVH8_PTEAL_9402 and tr_A0A2Y9K1H2_A0A2Y9K1H2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_L5JVH8_L5JVH8_PTEAL_9402 and tr_A0A384C4R5_A0A384C4R5_URSMA_29073 are exactly identical! WARNING: Sequences tr_L5JVH8_L5JVH8_PTEAL_9402 and tr_A0A383ZZ13_A0A383ZZ13_BALAS_310752 are exactly identical! WARNING: Sequences tr_M4ENB4_M4ENB4_BRARP_51351 and tr_A0A078FRU9_A0A078FRU9_BRANA_3708 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A0Q3MJ20_A0A0Q3MJ20_AMAAE_12930 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A091JHM1_A0A091JHM1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A093K4Z0_A0A093K4Z0_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A099ZUL0_A0A099ZUL0_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A0A0AWT3_A0A0A0AWT3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A093I4E2_A0A093I4E2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3IFI6_U3IFI6_ANAPL_8839 and tr_A0A091I9W9_A0A091I9W9_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A015KK77_A0A015KK77_9GLOM_1432141 and tr_A0A2I1DR50_A0A2I1DR50_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015KK77_A0A015KK77_9GLOM_1432141 and tr_A0A2H5S6Z8_A0A2H5S6Z8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0D3FM91_A0A0D3FM91_9ORYZ_65489 and tr_A0A0D9ZBD7_A0A0D9ZBD7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A067D6I7_A0A067D6I7_CITSI_2711 and tr_A0A067GC17_A0A067GC17_CITSI_2711 are exactly identical! WARNING: Sequences tr_A0A067D6I7_A0A067D6I7_CITSI_2711 and tr_V4SBW0_V4SBW0_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A096NE03_A0A096NE03_PAPAN_9555 and tr_A0A2K6C7A0_A0A2K6C7A0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NF50_A0A096NF50_PAPAN_9555 and tr_A0A2K6AP98_A0A2K6AP98_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091CTG3_A0A091CTG3_FUKDA_885580 and tr_A0A091DIT2_A0A091DIT2_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A091JL41_A0A091JL41_EGRGA_188379 and tr_A0A093HLK8_A0A093HLK8_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JL41_A0A091JL41_EGRGA_188379 and tr_A0A091XRK7_A0A091XRK7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091UWX1_A0A091UWX1_NIPNI_128390 and tr_A0A087RD46_A0A087RD46_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UWX1_A0A091UWX1_NIPNI_128390 and tr_A0A099YUT7_A0A099YUT7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091UWX1_A0A091UWX1_NIPNI_128390 and tr_A0A0A0AMP6_A0A0A0AMP6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091UWX1_A0A091UWX1_NIPNI_128390 and tr_A0A093GIF2_A0A093GIF2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VEE1_A0A091VEE1_NIPNI_128390 and tr_A0A087R358_A0A087R358_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A087RI20_A0A087RI20_APTFO_9233 and tr_A0A0A0ACA6_A0A0A0ACA6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091V5L1_A0A091V5L1_OPIHO_30419 and tr_A0A091GK85_A0A091GK85_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A2I0M4L5_A0A2I0M4L5_COLLI_8932 and tr_A0A1V4KYL9_A0A1V4KYL9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3ZI52_A0A1S3ZI52_TOBAC_4097 and tr_A0A1U7XL82_A0A1U7XL82_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AZM8_A0A1S4AZM8_TOBAC_4097 and tr_A0A1U7VTY2_A0A1U7VTY2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CRD6_A0A1S4CRD6_TOBAC_4097 and tr_A0A1U7YDT3_A0A1U7YDT3_NICSY_4096 are exactly identical! WARNING: Sequences tr_B5DGP8_B5DGP8_SALSA_8030 and tr_B5X2C8_B5X2C8_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2K5NPN9_A0A2K5NPN9_CERAT_9531 and tr_A0A2K5ZKQ4_A0A2K5ZKQ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U1KB93_A0A2U1KB93_ARTAN_35608 and tr_A0A2U1P6D6_A0A2U1P6D6_ARTAN_35608 are exactly identical! WARNING: Duplicate sequences found: 156 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/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.raxml.reduced.phy Alignment comprises 1 partitions and 1067 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1067 Gaps: 80.74 % Invariant sites: 32.90 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.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/Q8N7X1/3_mltree/Q8N7X1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 267 / 21360 [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: -120006.982011 [00:00:00 -120006.982011] Initial branch length optimization [00:00:04 -99656.762871] Model parameter optimization (eps = 0.100000) [00:02:09] Tree #1, final logLikelihood: -99147.855719 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.051990,0.191980) (0.060211,0.216070) (0.367898,0.767897) (0.519901,1.335834) 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/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7X1/4_raxmlng_ancestral/Q8N7X1.raxml.log Analysis started: 12-Jul-2021 18:10:57 / finished: 12-Jul-2021 18:13:18 Elapsed time: 140.899 seconds Consumed energy: 12.614 Wh