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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 17:52:21 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/2_msa/Q96S38_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/3_mltree/Q96S38.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622645541 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/020621_run/phylogeny-snakemake/results/Q96S38/2_msa/Q96S38_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1066 sites WARNING: Sequences tr_B4R442_B4R442_DROSI_7240 and tr_B4ILE1_B4ILE1_DROSE_7238 are exactly identical! WARNING: Sequences tr_F1P4J0_F1P4J0_CHICK_9031 and tr_A0A1V4K230_A0A1V4K230_PATFA_372326 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_D3Z8E0_D3Z8E0_RAT_10116 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_I3MFL8_I3MFL8_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A287A3K5_A0A287A3K5_PIG_9823 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2I2U9Z1_A0A2I2U9Z1_FELCA_9685 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A1U7QTC0_A0A1U7QTC0_MESAU_10036 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2U4AQL8_A0A2U4AQL8_TURTR_9739 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2U4AQM1_A0A2U4AQM1_TURTR_9739 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2U3W113_A0A2U3W113_ODORO_9708 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2U3YDK5_A0A2U3YDK5_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2Y9JRH9_A0A2Y9JRH9_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2Y9M3B9_A0A2Y9M3B9_DELLE_9749 are exactly identical! WARNING: Sequences sp_P18654_KS6A3_MOUSE_10090 and tr_A0A2Y9EK14_A0A2Y9EK14_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_M3YUR1_M3YUR1_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_G1QIR2_G1QIR2_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_G1P0P8_G1P0P8_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_H2NV94_H2NV94_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and sp_P67998_KS6B1_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_E2RMD8_E2RMD8_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_H2QDK7_H2QDK7_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_F7D5V6_F7D5V6_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and sp_P67999_KS6B1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_I3N8P3_I3N8P3_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and sp_P23443_KS6B1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_H9ENT4_H9ENT4_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_G3TCW7_G3TCW7_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_F7GCV0_F7GCV0_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_D2HLU3_D2HLU3_AILME_9646 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_F1MNP4_F1MNP4_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and sp_Q6TJY3_KS6B1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_M3X5V6_M3X5V6_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2I3LXQ2_A0A2I3LXQ2_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A091DJ72_A0A091DJ72_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A0D9R0Q9_A0A0D9R0Q9_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A1S3AEN3_A0A1S3AEN3_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A1S3EZE8_A0A1S3EZE8_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A1U7U9T8_A0A1U7U9T8_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2K5LA67_A0A2K5LA67_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2K6EAG2_A0A2K6EAG2_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2K5XVI9_A0A2K5XVI9_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2U4C5Z8_A0A2U4C5Z8_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2U4C601_A0A2U4C601_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2U3VRH2_A0A2U3VRH2_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2Y9DNR4_A0A2Y9DNR4_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2Y9K1P2_A0A2Y9K1P2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2Y9LI66_A0A2Y9LI66_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A2Y9FC81_A0A2Y9FC81_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A384CGY7_A0A384CGY7_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q8BSK8_KS6B1_MOUSE_10090 and tr_A0A384ASG2_A0A384ASG2_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1RDR9_G1RDR9_NOMLE_61853 and tr_G3QKB5_G3QKB5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RDR9_G1RDR9_NOMLE_61853 and tr_A0A2I3TPM9_A0A2I3TPM9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RDR9_G1RDR9_NOMLE_61853 and tr_F7H7W3_F7H7W3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RDR9_G1RDR9_NOMLE_61853 and tr_A0A2K6DY54_A0A2K6DY54_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RDR9_G1RDR9_NOMLE_61853 and tr_A0A2R9C536_A0A2R9C536_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_G3R0F8_G3R0F8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_H2PV35_H2PV35_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_K7DQL9_K7DQL9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and sp_P51812_KS6A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_U3D5H3_U3D5H3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_A0A2I3MWU5_A0A2I3MWU5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_A0A0D9RPY4_A0A0D9RPY4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RFU1_G1RFU1_NOMLE_61853 and tr_A0A2R9AC85_A0A2R9AC85_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3H5L5_G3H5L5_CRIGR_10029 and tr_E2RP04_E2RP04_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3H5L5_G3H5L5_CRIGR_10029 and tr_W5Q1L5_W5Q1L5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G3H5L5_G3H5L5_CRIGR_10029 and tr_A0A1U7U8F8_A0A1U7U8F8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3H5L5_G3H5L5_CRIGR_10029 and tr_A0A2U4AQL4_A0A2U4AQL4_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3H5L5_G3H5L5_CRIGR_10029 and tr_A0A2U4AQL6_A0A2U4AQL6_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_A0A2I3S8A4_A0A2I3S8A4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_A0A1D5QL06_A0A1D5QL06_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_F7GUI6_F7GUI6_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_A0A2K5KVU0_A0A2K5KVU0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_A0A2K6BBJ1_A0A2K6BBJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RK25_G3RK25_GORGO_9595 and tr_A0A2R8ZB76_A0A2R8ZB76_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PW53_H2PW53_PONAB_9601 and sp_Q9UK32_KS6A6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PW53_H2PW53_PONAB_9601 and tr_A0A096N856_A0A096N856_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PW53_H2PW53_PONAB_9601 and tr_A0A0D9RDU5_A0A0D9RDU5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A091JJT0_A0A091JJT0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A093SVE5_A0A093SVE5_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A091UMD8_A0A091UMD8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A087R029_A0A087R029_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A091VQM3_A0A091VQM3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A091GEY9_A0A091GEY9_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A0A0AEE6_A0A0A0AEE6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A093FYE4_A0A093FYE4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_G1N6A7_G1N6A7_MELGA_9103 and tr_A0A091HTV2_A0A091HTV2_CALAN_9244 are exactly identical! WARNING: Sequences tr_G1TIQ4_G1TIQ4_RABIT_9986 and tr_A0A2Y9DX92_A0A2Y9DX92_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2J8PJU5_A0A2J8PJU5_PANTR_9598 and tr_A0A2R9AEI3_A0A2R9AEI3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6TPX7_F6TPX7_ORNAN_9258 and tr_W5PYC2_W5PYC2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F7FRY0_F7FRY0_MONDO_13616 and tr_G3VW05_G3VW05_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A088A647_A0A088A647_APIME_7460 and tr_A0A2A3EKH5_A0A2A3EKH5_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NUR6_A0A158NUR6_ATTCE_12957 and tr_F4WE08_F4WE08_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NUR6_A0A158NUR6_ATTCE_12957 and tr_A0A151IV57_A0A151IV57_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NUR6_A0A158NUR6_ATTCE_12957 and tr_A0A195BBF4_A0A195BBF4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NUR6_A0A158NUR6_ATTCE_12957 and tr_A0A151K0I3_A0A151K0I3_9HYME_34720 are exactly identical! WARNING: Sequences sp_Q15418_KS6A1_HUMAN_9606 and tr_A0A0D9S842_A0A0D9S842_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9NRS6_SNX15_HUMAN_9606 and tr_A0A2R9BCC1_A0A2R9BCC1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UNV6_F6UNV6_MACMU_9544 and tr_A0A2K6AV95_A0A2K6AV95_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SUM7_E5SUM7_TRISP_6334 and tr_A0A0V0RNH0_A0A0V0RNH0_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SUM7_E5SUM7_TRISP_6334 and tr_A0A0V0V237_A0A0V0V237_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SUM7_E5SUM7_TRISP_6334 and tr_A0A0V0Z9Q2_A0A0V0Z9Q2_9BILA_990121 are exactly identical! WARNING: Sequences tr_H0ZBF2_H0ZBF2_TAEGU_59729 and tr_A0A218UU76_A0A218UU76_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7NUK8_G7NUK8_MACFA_9541 and tr_A0A2K6BI24_A0A2K6BI24_MACNE_9545 are exactly identical! WARNING: Sequences tr_U3JN67_U3JN67_FICAL_59894 and tr_A0A2I0MAS5_A0A2I0MAS5_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3KCS8_U3KCS8_FICAL_59894 and tr_A0A093PWE2_A0A093PWE2_9PASS_328815 are exactly identical! WARNING: Sequences tr_W2PK21_W2PK21_PHYPN_761204 and tr_A0A0W8CHP5_A0A0W8CHP5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PK21_W2PK21_PHYPN_761204 and tr_W2FWN5_W2FWN5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QJE2_W2QJE2_PHYPN_761204 and tr_W2LN77_W2LN77_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RC08_W2RC08_PHYPN_761204 and tr_W2NNQ5_W2NNQ5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NQA8_A0A096NQA8_PAPAN_9555 and tr_A0A2K6E0F6_A0A2K6E0F6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0K0ETV1_A0A0K0ETV1_STRVS_75913 and tr_A0A0N5B4F6_A0A0N5B4F6_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0K0DWU4_A0A0K0DWU4_STRER_6248 and tr_A0A090LI82_A0A090LI82_STRRB_34506 are exactly identical! WARNING: Sequences tr_A0A151M2M6_A0A151M2M6_ALLMI_8496 and tr_A0A3Q0HK21_A0A3Q0HK21_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3MT07_A0A0Q3MT07_AMAAE_12930 and tr_A0A2I0MU20_A0A2I0MU20_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0Q3MT07_A0A0Q3MT07_AMAAE_12930 and tr_A0A1V4JKY4_A0A1V4JKY4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0W8CA52_A0A0W8CA52_PHYNI_4790 and tr_W2KAV1_W2KAV1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A091IQI7_A0A091IQI7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A087RIY1_A0A087RIY1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A091WBC8_A0A091WBC8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A091FNE0_A0A091FNE0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A0A0AC81_A0A0A0AC81_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A093G661_A0A093G661_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091EBE2_A0A091EBE2_CORBR_85066 and tr_A0A091I022_A0A091I022_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091EBY0_A0A091EBY0_CORBR_85066 and tr_A0A091JB75_A0A091JB75_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091EBY0_A0A091EBY0_CORBR_85066 and tr_A0A091UL28_A0A091UL28_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EBY0_A0A091EBY0_CORBR_85066 and tr_A0A099YTE6_A0A099YTE6_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A087QXG3_A0A087QXG3_APTFO_9233 and tr_A0A091GB68_A0A091GB68_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093HL38_A0A093HL38_STRCA_441894 and tr_A0A099ZPR0_A0A099ZPR0_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V0X4G3_A0A0V0X4G3_9BILA_92179 and tr_A0A0V1L0M7_A0A0V1L0M7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1N813_A0A0V1N813_9BILA_268474 and tr_A0A0V1HKG5_A0A0V1HKG5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226MKA4_A0A226MKA4_CALSU_9009 and tr_A0A226P5F3_A0A226P5F3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1U8ER58_A0A1U8ER58_CAPAN_4072 and tr_A0A2G3BEG9_A0A2G3BEG9_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5LHW9_A0A2K5LHW9_CERAT_9531 and tr_A0A2K5XLD5_A0A2K5XLD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LWD1_A0A2K5LWD1_CERAT_9531 and tr_A0A2K6AEC4_A0A2K6AEC4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4AQK9_A0A2U4AQK9_TURTR_9739 and tr_A0A2U4AQL1_A0A2U4AQL1_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4AQK9_A0A2U4AQK9_TURTR_9739 and tr_A0A2U4AQL2_A0A2U4AQL2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4AQK9_A0A2U4AQK9_TURTR_9739 and tr_A0A2U4AQL3_A0A2U4AQL3_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4B3G5_A0A2U4B3G5_TURTR_9739 and tr_A0A2Y9NZM6_A0A2Y9NZM6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B3G5_A0A2U4B3G5_TURTR_9739 and tr_A0A2Y9T6P5_A0A2Y9T6P5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BL68_A0A2U4BL68_TURTR_9739 and tr_A0A2Y9LFC7_A0A2Y9LFC7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VIR8_A0A2U3VIR8_ODORO_9708 and tr_A0A384CD65_A0A384CD65_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 141 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.raxml.reduced.phy Alignment comprises 1 partitions and 1066 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1066 Gaps: 64.49 % Invariant sites: 0.09 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.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/020621_run/phylogeny-snakemake/results/Q96S38/3_mltree/Q96S38.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: -220448.241592 [00:00:00 -220448.241592] Initial branch length optimization [00:00:03 -191973.804799] Model parameter optimization (eps = 0.100000) [00:01:34] Tree #1, final logLikelihood: -191111.776535 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.128809,0.249872) (0.079889,0.394540) (0.334701,0.567127) (0.456601,1.634856) 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/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96S38/4_raxmlng_ancestral/Q96S38.raxml.log Analysis started: 02-Jun-2021 17:52:21 / finished: 02-Jun-2021 17:54:05 Elapsed time: 104.342 seconds Consumed energy: 6.525 Wh