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 04-Jun-2021 14:08:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/2_msa/Q13351_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/3_mltree/Q13351.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/4_raxmlng_ancestral/Q13351 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804930 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/Q13351/2_msa/Q13351_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 362 sites WARNING: Sequences sp_Q99JB0_KLF7_MOUSE_10090 and tr_G3HDK1_G3HDK1_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q99JB0_KLF7_MOUSE_10090 and tr_A0A3Q0CR77_A0A3Q0CR77_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G1PDP0_G1PDP0_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G3R1P0_G3R1P0_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_H2P8F1_H2P8F1_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2I3RAR5_A0A2I3RAR5_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_I3MGM2_I3MGM2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_H0XGM0_H0XGM0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and sp_O75840_KLF7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_F7HJI4_F7HJI4_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G5BH07_G5BH07_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_I3LBA7_I3LBA7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G1M9D9_G1M9D9_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G7PLA2_G7PLA2_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_E1BNF7_E1BNF7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_M3VYM9_M3VYM9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A096NXV9_A0A096NXV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A0D9RCL3_A0A0D9RCL3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2K5NKE7_A0A2K5NKE7_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2K6B622_A0A2K6B622_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2K5XC97_A0A2K5XC97_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2U3WAS6_A0A2U3WAS6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2U3Z1A2_A0A2U3Z1A2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2Y9DPM0_A0A2Y9DPM0_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2Y9MML2_A0A2Y9MML2_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2Y9SS03_A0A2Y9SS03_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A384BU08_A0A384BU08_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A384AU60_A0A384AU60_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_M3WQR5_M3WQR5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_A0A1S2ZQ80_A0A1S2ZQ80_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_A0A2U3VMG6_A0A2U3VMG6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_A0A2Y9JV30_A0A2Y9JV30_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y772_M3Y772_MUSPF_9669 and tr_A0A2U3WLG0_A0A2U3WLG0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y772_M3Y772_MUSPF_9669 and tr_A0A2Y9J7G8_A0A2Y9J7G8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_G3QYR3_G3QYR3_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_A0A2I3TQK3_A0A2I3TQK3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and sp_O95600_KLF8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_A0A2R9CQU0_A0A2R9CQU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GE53_A0A2I3GE53_NOMLE_61853 and tr_A0A2K5YA95_A0A2K5YA95_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RJY7_G1RJY7_NOMLE_61853 and tr_A0A2K6AAM1_A0A2K6AAM1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_G3QNE9_G3QNE9_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A2I3TG93_A0A2I3TG93_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and sp_Q9Y4X4_KLF12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_F6TF45_F6TF45_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_F7H530_F7H530_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_G7PVI4_G7PVI4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A096N0U2_A0A096N0U2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A2K5KKE2_A0A2K5KKE2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A2K6D8D3_A0A2K6D8D3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A2K5YAM7_A0A2K5YAM7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S221_G1S221_NOMLE_61853 and tr_A0A2R9ALE4_A0A2R9ALE4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_G3QPS2_G3QPS2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_H2PD38_H2PD38_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_H2QPC1_H2QPC1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and sp_P57682_KLF3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_F7E8X0_F7E8X0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_F7HPC0_F7HPC0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_G7P5E4_G7P5E4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_A0A096N246_A0A096N246_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_A0A0D9RWD1_A0A0D9RWD1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_A0A2K5KRZ1_A0A2K5KRZ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_A0A2K5ZGI8_A0A2K5ZGI8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S5B3_G1S5B3_NOMLE_61853 and tr_A0A2R8ZPC8_A0A2R8ZPC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NY31_G1NY31_MYOLU_59463 and tr_F7BJ35_F7BJ35_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PBD8_G1PBD8_MYOLU_59463 and tr_F6XU82_F6XU82_HORSE_9796 are exactly identical! WARNING: Sequences tr_G3GR84_G3GR84_CRIGR_10029 and tr_A0A1U7Q7G9_A0A1U7Q7G9_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QI26_G3QI26_GORGO_9595 and tr_H2N9M3_H2N9M3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QI26_G3QI26_GORGO_9595 and tr_A0A2I3SP65_A0A2I3SP65_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QI26_G3QI26_GORGO_9595 and sp_Q99612_KLF6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RWJ2_G3RWJ2_GORGO_9595 and tr_H2NK19_H2NK19_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RWJ2_G3RWJ2_GORGO_9595 and tr_A0A096N7X3_A0A096N7X3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RWJ2_G3RWJ2_GORGO_9595 and tr_A0A2K5LLH2_A0A2K5LLH2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RWJ2_G3RWJ2_GORGO_9595 and tr_A0A2K6BC77_A0A2K6BC77_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_H2PSZ2_H2PSZ2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_H2QXN2_H2QXN2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_F6VVB3_F6VVB3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_A0A0D9RG89_A0A0D9RG89_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_A0A2K5KZK9_A0A2K5KZK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SJ37_G3SJ37_GORGO_9595 and tr_A0A2K6BXA2_A0A2K6BXA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_J9P1H6_J9P1H6_CANLF_9615 and tr_G1M1J5_G1M1J5_AILME_9646 are exactly identical! WARNING: Sequences tr_J9P1H6_J9P1H6_CANLF_9615 and tr_M3WD25_M3WD25_FELCA_9685 are exactly identical! WARNING: Sequences tr_J9P1H6_J9P1H6_CANLF_9615 and tr_A0A2U3WRI2_A0A2U3WRI2_ODORO_9708 are exactly identical! WARNING: Sequences tr_J9P1H6_J9P1H6_CANLF_9615 and tr_A0A384BRT7_A0A384BRT7_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2QFH4_H2QFH4_PANTR_9598 and tr_A0A2R9BTB9_A0A2R9BTB9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CWI5_K7CWI5_PANTR_9598 and tr_H0XV81_H0XV81_OTOGA_30611 are exactly identical! WARNING: Sequences tr_K7CWI5_K7CWI5_PANTR_9598 and sp_Q9Y5W3_KLF2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CWI5_K7CWI5_PANTR_9598 and tr_A0A337SU48_A0A337SU48_FELCA_9685 are exactly identical! WARNING: Sequences tr_K7CWI5_K7CWI5_PANTR_9598 and tr_A0A0D9R0D3_A0A0D9R0D3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SME2_F6SME2_HORSE_9796 and tr_D2GZ24_D2GZ24_AILME_9646 are exactly identical! WARNING: Sequences tr_W5Q1P9_W5Q1P9_SHEEP_9940 and tr_A0A2U4A6V2_A0A2U4A6V2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A3B5QC05_A0A3B5QC05_XIPMA_8083 and tr_A0A087Y7B9_A0A087Y7B9_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5R4M9_A0A3B5R4M9_XIPMA_8083 and tr_A0A087X4S6_A0A087X4S6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_G8F2K4_G8F2K4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_A0A2K6BXQ6_A0A2K6BXQ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QQC6_A0A1D5QQC6_MACMU_9544 and tr_A0A0D9RYF3_A0A0D9RYF3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5REC6_A0A1D5REC6_MACMU_9544 and tr_A0A096P390_A0A096P390_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5REC6_A0A1D5REC6_MACMU_9544 and tr_A0A0D9RNA8_A0A0D9RNA8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5REC6_A0A1D5REC6_MACMU_9544 and tr_A0A2K5M6H6_A0A2K5M6H6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5REC6_A0A1D5REC6_MACMU_9544 and tr_A0A2K6BW57_A0A2K6BW57_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3THQ8_G3THQ8_LOXAF_9785 and tr_F1MQF5_F1MQF5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3THQ8_G3THQ8_LOXAF_9785 and tr_A0A384AG11_A0A384AG11_BALAS_310752 are exactly identical! WARNING: Sequences tr_H0YR03_H0YR03_TAEGU_59729 and tr_A0A218UFL4_A0A218UFL4_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0YRM0_H0YRM0_TAEGU_59729 and tr_A0A091F2I3_A0A091F2I3_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZFG3_H0ZFG3_TAEGU_59729 and tr_A0A218ULR7_A0A218ULR7_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A287APC5_A0A287APC5_PIG_9823 and tr_A0A2Y9JDK4_A0A2Y9JDK4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3JN03_U3JN03_FICAL_59894 and tr_A0A218UHV8_A0A218UHV8_9PASE_299123 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A093QKC2_A0A093QKC2_9PASS_328815 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A091UP63_A0A091UP63_NIPNI_128390 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A087R0T7_A0A087R0T7_APTFO_9233 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A099ZMC1_A0A099ZMC1_TINGU_94827 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A0A0A1V1_A0A0A0A1V1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A2I0MQ45_A0A2I0MQ45_COLLI_8932 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A091IIT3_A0A091IIT3_CALAN_9244 are exactly identical! WARNING: Sequences tr_R0LNM6_R0LNM6_ANAPL_8839 and tr_A0A1V4KLN9_A0A1V4KLN9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A151PD38_A0A151PD38_ALLMI_8496 and tr_A0A1U7RUE7_A0A1U7RUE7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A093QBM2_A0A093QBM2_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A091UQ94_A0A091UQ94_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A091V7Z2_A0A091V7Z2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A0A0ASZ6_A0A0A0ASZ6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091J374_A0A091J374_EGRGA_188379 and tr_A0A093SMD8_A0A093SMD8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091J374_A0A091J374_EGRGA_188379 and tr_A0A091UYH0_A0A091UYH0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J374_A0A091J374_EGRGA_188379 and tr_A0A087R6R1_A0A087R6R1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J374_A0A091J374_EGRGA_188379 and tr_A0A091FU83_A0A091FU83_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091J3I8_A0A091J3I8_EGRGA_188379 and tr_A0A091V171_A0A091V171_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J3I8_A0A091J3I8_EGRGA_188379 and tr_A0A087R6R2_A0A087R6R2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J3I8_A0A091J3I8_EGRGA_188379 and tr_A0A091FPX4_A0A091FPX4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093Q9F1_A0A093Q9F1_9PASS_328815 and tr_A0A087QJW1_A0A087QJW1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VD14_A0A091VD14_NIPNI_128390 and tr_A0A093GNW9_A0A093GNW9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VD14_A0A091VD14_NIPNI_128390 and tr_A0A091HTT4_A0A091HTT4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091WE98_A0A091WE98_OPIHO_30419 and tr_A0A093G393_A0A093G393_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091XJW4_A0A091XJW4_OPIHO_30419 and tr_A0A0A0ADP8_A0A0A0ADP8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LXM2_A0A2I0LXM2_COLLI_8932 and tr_A0A1V4L0Q7_A0A1V4L0Q7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CKA4_A0A0V1CKA4_TRIBR_45882 and tr_A0A0V1LHE9_A0A0V1LHE9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2K5NXJ2_A0A2K5NXJ2_CERAT_9531 and tr_A0A2K6BZU6_A0A2K6BZU6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5YCK9_A0A2K5YCK9_MANLE_9568 and tr_A0A2R9AAJ4_A0A2R9AAJ4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2U3V1D2_A0A2U3V1D2_TURTR_9739 and tr_A0A2Y9NUE9_A0A2Y9NUE9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A0Z8_A0A2U4A0Z8_TURTR_9739 and tr_A0A2Y9MJU6_A0A2Y9MJU6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A7A7_A0A2U4A7A7_TURTR_9739 and tr_A0A2Y9NN38_A0A2Y9NN38_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4ASJ0_A0A2U4ASJ0_TURTR_9739 and tr_A0A2Y9MLJ4_A0A2Y9MLJ4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B6N6_A0A2U4B6N6_TURTR_9739 and tr_A0A2Y9MI15_A0A2Y9MI15_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B6N6_A0A2U4B6N6_TURTR_9739 and tr_A0A383YXB5_A0A383YXB5_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3YAQ4_A0A2U3YAQ4_LEPWE_9713 and tr_A0A384BQK2_A0A384BQK2_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2Y9KYU4_A0A2Y9KYU4_ENHLU_391180 and tr_A0A384D9G2_A0A384D9G2_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2Y9LXB9_A0A2Y9LXB9_DELLE_9749 and tr_A0A2Y9TI56_A0A2Y9TI56_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 144 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/Q13351/4_raxmlng_ancestral/Q13351.raxml.reduced.phy Alignment comprises 1 partitions and 362 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 362 Gaps: 44.58 % Invariant sites: 6.08 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/4_raxmlng_ancestral/Q13351.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/Q13351/3_mltree/Q13351.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 91 / 7280 [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: -183631.308893 [00:00:00 -183631.308893] Initial branch length optimization [00:00:01 -97866.388820] Model parameter optimization (eps = 0.100000) [00:00:30] Tree #1, final logLikelihood: -97665.013259 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.103636,0.085452) (0.115313,0.131003) (0.222002,0.686286) (0.559048,1.473362) 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/Q13351/4_raxmlng_ancestral/Q13351.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/4_raxmlng_ancestral/Q13351.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/4_raxmlng_ancestral/Q13351.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13351/4_raxmlng_ancestral/Q13351.raxml.log Analysis started: 04-Jun-2021 14:08:50 / finished: 04-Jun-2021 14:09:24 Elapsed time: 34.018 seconds