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 03-Jun-2021 02:13:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/2_msa/P26367_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/3_mltree/P26367.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/4_raxmlng_ancestral/P26367 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675607 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/P26367/2_msa/P26367_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 422 sites WARNING: Sequences tr_B4QD60_B4QD60_DROSI_7240 and tr_B4IHC7_B4IHC7_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q9PTX1_Q9PTX1_CHICK_9031 and tr_A0A093PXS7_A0A093PXS7_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q9PTX1_Q9PTX1_CHICK_9031 and tr_A0A091ULF2_A0A091ULF2_NIPNI_128390 are exactly identical! WARNING: Sequences sp_P47239_PAX7_MOUSE_10090 and tr_A0A1U7QKY1_A0A1U7QKY1_MESAU_10036 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_M3YIP6_M3YIP6_MUSPF_9669 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_G1P774_G1P774_MYOLU_59463 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A2J8P473_A0A2J8P473_PANTR_9598 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_I3M1V0_I3M1V0_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and sp_P26367_PAX6_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_F7C9W0_F7C9W0_MACMU_9544 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A0D9QYX8_A0A0D9QYX8_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A1S3A6H0_A0A1S3A6H0_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A2U3WCG3_A0A2U3WCG3_ODORO_9708 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A2Y9D8A2_A0A2Y9D8A2_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P63015_PAX6_MOUSE_10090 and tr_A0A2Y9JMR1_A0A2Y9JMR1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and tr_H2N8U5_H2N8U5_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and tr_H2PY64_H2PY64_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and sp_P23759_PAX7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and tr_F7HMI2_F7HMI2_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and tr_A0A2K5ZL55_A0A2K5ZL55_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YXN8_M3YXN8_MUSPF_9669 and tr_A0A2Y9KME0_A0A2Y9KME0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_G1PPE9_G1PPE9_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_F7DM34_F7DM34_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_I3LAG7_I3LAG7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_F1MTX0_F1MTX0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_A0A2U3WFS5_A0A2U3WFS5_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_A0A2U3YIS4_A0A2U3YIS4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YZ10_M3YZ10_MUSPF_9669 and tr_A0A2Y9IZL0_A0A2Y9IZL0_ENHLU_391180 are exactly identical! WARNING: Sequences sp_O73917_PAX6_ORYLA_8090 and tr_A0A087YGE4_A0A087YGE4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and tr_G3RHY0_G3RHY0_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and sp_P23760_PAX3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and tr_F6U1Q1_F6U1Q1_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and tr_A0A2K5MN68_A0A2K5MN68_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and tr_A0A2K6DMI1_A0A2K6DMI1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3G0R2_A0A2I3G0R2_NOMLE_61853 and tr_A0A2R9B452_A0A2R9B452_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A2J8SH69_A0A2J8SH69_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A2J8IVS0_A0A2J8IVS0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_H0X0J0_H0X0J0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and sp_Q06710_PAX8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A1D5Q7A9_A0A1D5Q7A9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A096MUZ8_A0A096MUZ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A0D9RVU8_A0A0D9RVU8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A2K5MMG9_A0A2K5MMG9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A2K6CT02_A0A2K6CT02_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Y654_A0A2I2Y654_GORGO_9595 and tr_A0A2R9AHH6_A0A2R9AHH6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QNL3_G3QNL3_GORGO_9595 and tr_G7NUS0_G7NUS0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QNL3_G3QNL3_GORGO_9595 and tr_A0A2K6CHJ7_A0A2K6CHJ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2P8Q9_H2P8Q9_PONAB_9601 and tr_A0A2I3TNC5_A0A2I3TNC5_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P8Q9_H2P8Q9_PONAB_9601 and tr_A0A0D9R641_A0A0D9R641_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_H2R6P1_H2R6P1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_I3NDD8_I3NDD8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_H0VFV1_H0VFV1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and sp_Q02548_PAX5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_G7NF13_G7NF13_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_F6SUH6_F6SUH6_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_G7PRX3_G7PRX3_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_A0A0D9REC5_A0A0D9REC5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_A0A1U7UU97_A0A1U7UU97_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2PRQ3_H2PRQ3_PONAB_9601 and tr_A0A3Q0D5T7_A0A3Q0D5T7_MESAU_10036 are exactly identical! WARNING: Sequences tr_H9GH42_H9GH42_ANOCA_28377 and tr_A0A226MWT9_A0A226MWT9_CALSU_9009 are exactly identical! WARNING: Sequences tr_B5DRZ9_B5DRZ9_DROPS_46245 and tr_B4HC93_B4HC93_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q28Z89_Q28Z89_DROPS_46245 and tr_B4GI33_B4GI33_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29CU9_Q29CU9_DROPS_46245 and tr_B4H894_B4H894_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RIS8_E2RIS8_CANLF_9615 and tr_G1LU97_G1LU97_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RIS8_E2RIS8_CANLF_9615 and tr_A0A2U3VD65_A0A2U3VD65_ODORO_9708 are exactly identical! WARNING: Sequences sp_P47240_PAX8_CANLF_9615 and tr_A0A2U3WXH1_A0A2U3WXH1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_I3MHL2_I3MHL2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and sp_Q02962_PAX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_F7HRH6_F7HRH6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A2R8M8G3_A0A2R8M8G3_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A286ZI72_A0A286ZI72_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_F1MNR2_F1MNR2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A2K5NCI4_A0A2K5NCI4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A2K6EBG9_A0A2K6EBG9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A2K5ZNU3_A0A2K5ZNU3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3TPA8_A0A2I3TPA8_PANTR_9598 and tr_A0A2R8Z8G7_A0A2R8Z8G7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QVB3_H2QVB3_PANTR_9598 and tr_A0A2R9AS32_A0A2R9AS32_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q3U7_W5Q3U7_SHEEP_9940 and sp_Q1LZF1_PAX6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158NXR3_A0A158NXR3_ATTCE_12957 and tr_F4WTH3_F4WTH3_ACREC_103372 are exactly identical! WARNING: Sequences tr_H0WQN3_H0WQN3_OTOGA_30611 and tr_A0A2K5Y6U0_A0A2K5Y6U0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0WX77_H0WX77_OTOGA_30611 and tr_G7PQH1_G7PQH1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BGZ5_F7BGZ5_XENTR_8364 and tr_A0A1L8FJY5_A0A1L8FJY5_XENLA_8355 are exactly identical! WARNING: Sequences tr_B4MF41_B4MF41_DROVI_7244 and tr_D0Z7E2_D0Z7E2_DROVI_7244 are exactly identical! WARNING: Sequences tr_L5JRP7_L5JRP7_PTEAL_9402 and tr_A0A337S438_A0A337S438_FELCA_9685 are exactly identical! WARNING: Sequences tr_L5JRP7_L5JRP7_PTEAL_9402 and tr_A0A096P695_A0A096P695_PAPAN_9555 are exactly identical! WARNING: Sequences tr_L5JRP7_L5JRP7_PTEAL_9402 and tr_A0A1S3F9Q0_A0A1S3F9Q0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_L5JRP7_L5JRP7_PTEAL_9402 and tr_A0A2U3W1Z1_A0A2U3W1Z1_ODORO_9708 are exactly identical! WARNING: Sequences tr_L5JRP7_L5JRP7_PTEAL_9402 and tr_A0A2Y9J6W4_A0A2Y9J6W4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A044THY8_A0A044THY8_ONCVO_6282 and tr_A0A182DZ45_A0A182DZ45_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0K0FH33_A0A0K0FH33_STRVS_75913 and tr_A0A0N5C9T9_A0A0N5C9T9_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A026W9X6_A0A026W9X6_OOCBI_2015173 and tr_A0A195DYE3_A0A195DYE3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A026W9X6_A0A026W9X6_OOCBI_2015173 and tr_A0A195B7I8_A0A195B7I8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A194RC13_A0A194RC13_PAPMA_76193 and tr_A0A194Q439_A0A194Q439_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A091G3D2_A0A091G3D2_9AVES_55661 and tr_A0A093GMI3_A0A093GMI3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091G3D2_A0A091G3D2_9AVES_55661 and tr_A0A091HNQ7_A0A091HNQ7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V1DAX5_A0A0V1DAX5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V0WN25_A0A0V0WN25_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V0VH70_A0A0V0VH70_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V1LJA7_A0A0V1LJA7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V1PJK5_A0A0V1PJK5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SGM3_A0A0V0SGM3_9BILA_6336 and tr_A0A0V0UG43_A0A0V0UG43_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V0X2M4_A0A0V0X2M4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V0VEU6_A0A0V0VEU6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V1KW01_A0A0V1KW01_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V1AD43_A0A0V1AD43_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V1PC15_A0A0V1PC15_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CFS6_A0A0V1CFS6_TRIBR_45882 and tr_A0A0V0TKW0_A0A0V0TKW0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S2ZT52_A0A1S2ZT52_ERIEU_9365 and tr_A0A2Y9JGI1_A0A2Y9JGI1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A1S3KZ54_A0A1S3KZ54_SALSA_8030 and tr_A0A1S3N5S7_A0A1S3N5S7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3KZ54_A0A1S3KZ54_SALSA_8030 and tr_A0A1S3QWV8_A0A1S3QWV8_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A0M4E1R7_A0A0M4E1R7_DROBS_30019 and tr_A0A0M4EDQ1_A0A0M4EDQ1_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A1D1W3C6_A0A1D1W3C6_RAMVA_947166 and tr_A0A1D1W5C8_A0A1D1W5C8_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226N0H6_A0A226N0H6_CALSU_9009 and tr_A0A226P567_A0A226P567_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QMJ1_A0A2D0QMJ1_ICTPU_7998 and tr_A0A2D0QMV3_A0A2D0QMV3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMJ1_A0A2D0QMJ1_ICTPU_7998 and tr_A0A2D0QQI6_A0A2D0QQI6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMJ7_A0A2D0QMJ7_ICTPU_7998 and tr_A0A2D0QQJ0_A0A2D0QQJ0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMK1_A0A2D0QMK1_ICTPU_7998 and tr_A0A2D0QMW0_A0A2D0QMW0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMK1_A0A2D0QMK1_ICTPU_7998 and tr_A0A2D0QPS6_A0A2D0QPS6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMK1_A0A2D0QMK1_ICTPU_7998 and tr_A0A2D0QPS8_A0A2D0QPS8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMK6_A0A2D0QMK6_ICTPU_7998 and tr_A0A2D0QN56_A0A2D0QN56_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMX2_A0A2D0QMX2_ICTPU_7998 and tr_A0A2D0QQJ8_A0A2D0QQJ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QN46_A0A2D0QN46_ICTPU_7998 and tr_A0A2D0QPS1_A0A2D0QPS1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QN51_A0A2D0QN51_ICTPU_7998 and tr_A0A2D0QPT3_A0A2D0QPT3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QN60_A0A2D0QN60_ICTPU_7998 and tr_A0A2D0QQJ4_A0A2D0QQJ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REG7_A0A2D0REG7_ICTPU_7998 and tr_A0A2D0REH3_A0A2D0REH3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REG7_A0A2D0REG7_ICTPU_7998 and tr_A0A2D0RFN2_A0A2D0RFN2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REG7_A0A2D0REG7_ICTPU_7998 and tr_A0A2D0RGB7_A0A2D0RGB7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REG7_A0A2D0REG7_ICTPU_7998 and tr_W5UL24_W5UL24_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REG8_A0A2D0REG8_ICTPU_7998 and tr_A0A2D0REJ0_A0A2D0REJ0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K6CL33_A0A2K6CL33_MACNE_9545 and tr_A0A2K5Y8E8_A0A2K5Y8E8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9MNE1_A0A2Y9MNE1_DELLE_9749 and tr_A0A2Y9EP31_A0A2Y9EP31_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MNE1_A0A2Y9MNE1_DELLE_9749 and tr_A0A384AL18_A0A384AL18_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9MQY4_A0A2Y9MQY4_DELLE_9749 and tr_A0A2Y9EHC3_A0A2Y9EHC3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MQY4_A0A2Y9MQY4_DELLE_9749 and tr_A0A384AJ74_A0A384AJ74_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9P7V1_A0A2Y9P7V1_DELLE_9749 and tr_A0A384A1M2_A0A384A1M2_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9FP06_A0A2Y9FP06_PHYCD_9755 and tr_A0A384BBL6_A0A384BBL6_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 136 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/P26367/4_raxmlng_ancestral/P26367.raxml.reduced.phy Alignment comprises 1 partitions and 422 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 422 Gaps: 30.26 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/4_raxmlng_ancestral/P26367.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/P26367/3_mltree/P26367.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 106 / 8480 [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: -123917.581558 [00:00:00 -123917.581558] Initial branch length optimization [00:00:01 -103595.856935] Model parameter optimization (eps = 0.100000) [00:01:17] Tree #1, final logLikelihood: -103297.849743 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.159857,0.179730) (0.160464,1.064270) (0.197332,0.414628) (0.482346,1.489952) 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/P26367/4_raxmlng_ancestral/P26367.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/4_raxmlng_ancestral/P26367.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/4_raxmlng_ancestral/P26367.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P26367/4_raxmlng_ancestral/P26367.raxml.log Analysis started: 03-Jun-2021 02:13:27 / finished: 03-Jun-2021 02:14:48 Elapsed time: 81.236 seconds Consumed energy: 6.011 Wh