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 17:57:44 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/2_msa/P52945_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/3_mltree/P52945.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/4_raxmlng_ancestral/P52945 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101864 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/P52945/2_msa/P52945_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 283 sites WARNING: Sequences tr_A0A1D5PE06_A0A1D5PE06_CHICK_9031 and tr_A0A226N8K1_A0A226N8K1_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1BZG3_E1BZG3_CHICK_9031 and tr_A0A226NEX8_A0A226NEX8_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1BZG3_E1BZG3_CHICK_9031 and tr_A0A226PEX2_A0A226PEX2_COLVI_9014 are exactly identical! WARNING: Sequences sp_P14840_HXB4_CHICK_9031 and tr_A0A226N7W7_A0A226N7W7_CALSU_9009 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_G3QGY7_G3QGY7_GORGO_9595 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_H2Q635_H2Q635_PANTR_9598 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_G3V841_G3V841_RAT_10116 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and sp_P09630_HXC6_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2R8M6J4_A0A2R8M6J4_CALJA_9483 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_G7PHW2_G7PHW2_MACFA_9541 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2I3MZ73_A0A2I3MZ73_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A0D9QZH0_A0A0D9QZH0_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2K5KJS2_A0A2K5KJS2_CERAT_9531 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2K6C6L8_A0A2K6C6L8_MACNE_9545 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2K5XCH5_A0A2K5XCH5_MANLE_9568 are exactly identical! WARNING: Sequences sp_P10629_HXC6_MOUSE_10090 and tr_A0A2R9BDQ6_A0A2R9BDQ6_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_G1S7G0_G1S7G0_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2I2Z6R8_A0A2I2Z6R8_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_E2QSM9_E2QSM9_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2I3SAW3_A0A2I3SAW3_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_I3N4H2_I3N4H2_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and sp_P09017_HXC4_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A287BEN5_A0A287BEN5_PIG_9823 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_D2HM48_D2HM48_AILME_9646 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A4FUC1_A4FUC1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_L5L6B5_L5L6B5_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2I2ULB3_A0A2I2ULB3_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A096N4V5_A0A096N4V5_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A0D9QZG7_A0A0D9QZG7_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A1S3GIZ1_A0A1S3GIZ1_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A1U8BK99_A0A1U8BK99_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2K5MMI7_A0A2K5MMI7_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2K6D2U9_A0A2K6D2U9_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2K5XBC7_A0A2K5XBC7_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2R9BS03_A0A2R9BS03_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2U3UYC3_A0A2U3UYC3_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2Y9DG31_A0A2Y9DG31_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2Y9KQ47_A0A2Y9KQ47_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q08624_HXC4_MOUSE_10090 and tr_A0A2Y9FL63_A0A2Y9FL63_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Y039_M3Y039_MUSPF_9669 and tr_F1SHT1_F1SHT1_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Y039_M3Y039_MUSPF_9669 and tr_A0A2U3VQF2_A0A2U3VQF2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y039_M3Y039_MUSPF_9669 and tr_A0A2U3XNN4_A0A2U3XNN4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y039_M3Y039_MUSPF_9669 and tr_A0A2Y9JCM5_A0A2Y9JCM5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_G1QE21_G1QE21_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_G3QIH3_G3QIH3_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_H2PMK4_H2PMK4_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_E2R5W8_E2R5W8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_H2QUB6_H2QUB6_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_F7DK44_F7DK44_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_I3MGW0_I3MGW0_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and sp_P20719_HXA5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_B0VXK6_B0VXK6_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_E1U314_E1U314_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and sp_Q2HJ67_HXA5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A337SUM0_A0A337SUM0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A9L940_A9L940_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A0D9RP77_A0A0D9RP77_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A1S2ZZC2_A0A1S2ZZC2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A1S3FVT8_A0A1S3FVT8_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2K5NYP2_A0A2K5NYP2_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2K6DNI0_A0A2K6DNI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2R9CM15_A0A2R9CM15_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2U3VQF3_A0A2U3VQF3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2U3XNM2_A0A2U3XNM2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2Y9JGL2_A0A2Y9JGL2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2Y9P4W7_A0A2Y9P4W7_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A2Y9F0M7_A0A2Y9F0M7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Y081_M3Y081_MUSPF_9669 and tr_A0A383Z9K4_A0A383Z9K4_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YRK5_M3YRK5_MUSPF_9669 and tr_A0A2Y9J0Z6_A0A2Y9J0Z6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P09077_SCR_DROME_7227 and tr_A0A1W4UU41_A0A1W4UU41_DROFC_30025 are exactly identical! WARNING: Sequences tr_I6L4S4_I6L4S4_ORYLA_8090 and sp_Q3V5Z9_HXD3_ORYLA_8090 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_H2NVH6_H2NVH6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_H2QDC0_H2QDC0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and sp_P17483_HXB4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_A0A096P424_A0A096P424_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_A0A0D9S3S5_A0A0D9S3S5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_A0A2K5NEG8_A0A2K5NEG8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_A0A2K6BZM8_A0A2K6BZM8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QQ82_G1QQ82_NOMLE_61853 and tr_A0A2R9C1W2_A0A2R9C1W2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Z5T2_A0A2I2Z5T2_GORGO_9595 and tr_H2QJ13_H2QJ13_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z5T2_A0A2I2Z5T2_GORGO_9595 and tr_A0A2R9AIR2_A0A2R9AIR2_PANPA_9597 are exactly identical! WARNING: Sequences sp_A1YER7_HXD4_GORGO_9595 and sp_A2T6X6_HXD4_PANTR_9598 are exactly identical! WARNING: Sequences sp_A1YER7_HXD4_GORGO_9595 and sp_P09016_HXD4_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A1YER7_HXD4_GORGO_9595 and sp_A1YFY3_HXD4_PANPA_9597 are exactly identical! WARNING: Sequences sp_A1YF08_PDX1_GORGO_9595 and sp_P52945_PDX1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QIG8_G3QIG8_GORGO_9595 and tr_H2QUB5_H2QUB5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QIG8_G3QIG8_GORGO_9595 and tr_A0A2R9AND9_A0A2R9AND9_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q296U7_Q296U7_DROPS_46245 and tr_B4GEM6_B4GEM6_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RGV4_E2RGV4_CANLF_9615 and tr_A0A2U3WJQ4_A0A2U3WJQ4_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RGV4_E2RGV4_CANLF_9615 and tr_A0A2U3Y797_A0A2U3Y797_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A3B5Q1A8_A0A3B5Q1A8_XIPMA_8083 and tr_A0A087Y7M4_A0A087Y7M4_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZFP6_M3ZFP6_XIPMA_8083 and tr_A0A096MIL9_A0A096MIL9_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NAC0_A0A158NAC0_ATTCE_12957 and tr_A0A151X2H6_A0A151X2H6_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NAC0_A0A158NAC0_ATTCE_12957 and tr_A0A151I046_A0A151I046_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3K2S4_I3K2S4_ORENI_8128 and tr_A0A2I4C1R1_A0A2I4C1R1_9TELE_52670 are exactly identical! WARNING: Sequences tr_H0XVF3_H0XVF3_OTOGA_30611 and tr_A0A1U7TDG8_A0A1U7TDG8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A286XF93_A0A286XF93_CAVPO_10141 and tr_G5BIE0_G5BIE0_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A1D5QLF7_A0A1D5QLF7_MACMU_9544 and tr_A0A2K6BZL1_A0A2K6BZL1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E256_F7E256_MACMU_9544 and tr_A0A2K5NL36_A0A2K5NL36_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E256_F7E256_MACMU_9544 and tr_A0A2K6BP52_A0A2K6BP52_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E256_F7E256_MACMU_9544 and tr_A0A2K5XQA5_A0A2K5XQA5_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YXG2_H0YXG2_TAEGU_59729 and tr_A0A218VDU3_A0A218VDU3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZF69_H0ZF69_TAEGU_59729 and tr_A0A091ETP0_A0A091ETP0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZF69_H0ZF69_TAEGU_59729 and tr_A0A093QSG6_A0A093QSG6_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZF69_H0ZF69_TAEGU_59729 and tr_A0A091VZ90_A0A091VZ90_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZF69_H0ZF69_TAEGU_59729 and tr_A0A0A0A0H8_A0A0A0A0H8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZF69_H0ZF69_TAEGU_59729 and tr_A0A218V0N8_A0A218V0N8_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WNA5_F4WNA5_ACREC_103372 and tr_A0A195EW58_A0A195EW58_9HYME_34720 are exactly identical! WARNING: Sequences tr_G7PKW6_G7PKW6_MACFA_9541 and tr_A0A096N3X1_A0A096N3X1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PKW6_G7PKW6_MACFA_9541 and tr_A0A2K5LB87_A0A2K5LB87_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PKW6_G7PKW6_MACFA_9541 and tr_A0A2K6DDH9_A0A2K6DDH9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PKW6_G7PKW6_MACFA_9541 and tr_A0A2K5ZEF4_A0A2K5ZEF4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A337RUD2_A0A337RUD2_FELCA_9685 and tr_A0A2U3VJU1_A0A2U3VJU1_ODORO_9708 are exactly identical! WARNING: Sequences tr_U3K4B5_U3K4B5_FICAL_59894 and tr_A0A087R7A6_A0A087R7A6_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3K4B5_U3K4B5_FICAL_59894 and tr_A0A2I0MR32_A0A2I0MR32_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3K4B5_U3K4B5_FICAL_59894 and tr_A0A218VDV2_A0A218VDV2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I3NDR6_A0A2I3NDR6_PAPAN_9555 and tr_A0A2K5LMF8_A0A2K5LMF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NDR6_A0A2I3NDR6_PAPAN_9555 and tr_A0A2K5XSF4_A0A2K5XSF4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0F763_A0A0K0F763_STRVS_75913 and tr_A0A0N5BVM2_A0A0N5BVM2_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A091J9B6_A0A091J9B6_EGRGA_188379 and tr_A0A091GDP6_A0A091GDP6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093QG27_A0A093QG27_9PASS_328815 and tr_A0A091UIS8_A0A091UIS8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093QG27_A0A093QG27_9PASS_328815 and tr_A0A087R099_A0A087R099_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093QG27_A0A093QG27_9PASS_328815 and tr_A0A0A0AHN9_A0A0A0AHN9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093QG27_A0A093QG27_9PASS_328815 and tr_A0A093G7I0_A0A093G7I0_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091G0Q8_A0A091G0Q8_9AVES_55661 and tr_A0A0A0ALZ5_A0A0A0ALZ5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091GDK0_A0A091GDK0_9AVES_55661 and tr_A0A091IK20_A0A091IK20_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0RUW2_A0A0V0RUW2_9BILA_6336 and tr_A0A0V0ZSQ1_A0A0V0ZSQ1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DG56_A0A0V1DG56_TRIBR_45882 and tr_A0A0V0VHK1_A0A0V0VHK1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DG56_A0A0V1DG56_TRIBR_45882 and tr_A0A0V1P5K6_A0A0V1P5K6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DG56_A0A0V1DG56_TRIBR_45882 and tr_A0A0V0UG57_A0A0V0UG57_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3M563_A0A1S3M563_SALSA_8030 and tr_B3SUC5_B3SUC5_SALSA_8030 are exactly identical! WARNING: Sequences tr_B3SU75_B3SU75_SALSA_8030 and tr_A0A060W4J5_A0A060W4J5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_B3SUC3_B3SUC3_SALSA_8030 and tr_A0A060YYI9_A0A060YYI9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_B3TDC6_B3TDC6_SALSA_8030 and tr_A0A060W481_A0A060W481_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MFR8_A0A226MFR8_CALSU_9009 and tr_A0A226PN27_A0A226PN27_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MYM8_A0A226MYM8_CALSU_9009 and tr_A0A226P1L4_A0A226P1L4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MZ17_A0A226MZ17_CALSU_9009 and tr_A0A226P0K7_A0A226P0K7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5MD41_A0A2K5MD41_CERAT_9531 and tr_A0A2K6EBK0_A0A2K6EBK0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5MH70_A0A2K5MH70_CERAT_9531 and tr_A0A2K5YL01_A0A2K5YL01_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3UYM9_A0A2U3UYM9_TURTR_9739 and tr_A0A2Y9NEN6_A0A2Y9NEN6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4ALW2_A0A2U4ALW2_TURTR_9739 and tr_A0A2Y9PAD0_A0A2Y9PAD0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WJP9_A0A2U3WJP9_ODORO_9708 and tr_A0A2U3Y790_A0A2U3Y790_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9EVF9_A0A2Y9EVF9_PHYCD_9755 and tr_A0A383ZMU3_A0A383ZMU3_BALAS_310752 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/P52945/4_raxmlng_ancestral/P52945.raxml.reduced.phy Alignment comprises 1 partitions and 283 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 283 Gaps: 40.08 % Invariant sites: 4.95 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/4_raxmlng_ancestral/P52945.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/P52945/3_mltree/P52945.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 71 / 5680 [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: -249248.832838 [00:00:00 -249248.832838] Initial branch length optimization [00:00:02 -96885.929390] Model parameter optimization (eps = 0.100000) [00:01:38] Tree #1, final logLikelihood: -95289.076134 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.254069,1.816413) (0.182742,0.014367) (0.202593,0.270293) (0.360595,1.334239) 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/P52945/4_raxmlng_ancestral/P52945.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/4_raxmlng_ancestral/P52945.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/4_raxmlng_ancestral/P52945.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52945/4_raxmlng_ancestral/P52945.raxml.log Analysis started: 12-Jul-2021 17:57:44 / finished: 12-Jul-2021 17:59:25 Elapsed time: 101.537 seconds Consumed energy: 9.568 Wh