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 19-Jun-2021 19:56:56 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/2_msa/Q15475_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/3_mltree/Q15475.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624121816 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_040621/phylogeny-snakemake/results/Q15475/2_msa/Q15475_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 284 sites WARNING: Sequences tr_B4QJ70_B4QJ70_DROSI_7240 and tr_Q9Y1P6_Q9Y1P6_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QJ70_B4QJ70_DROSI_7240 and tr_B3M9T2_B3M9T2_DROAN_7217 are exactly identical! WARNING: Sequences tr_B4QJ70_B4QJ70_DROSI_7240 and tr_A0A1W4VBC8_A0A1W4VBC8_DROFC_30025 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and sp_P40427_EXD_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_B4JX43_B4JX43_DROGR_7222 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_B4IMG8_B4IMG8_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_B4MT87_B4MT87_DROWI_7260 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_B4MA61_B4MA61_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_B4MAH8_B4MAH8_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_A0A0M4ESN1_A0A0M4ESN1_DROBS_30019 are exactly identical! WARNING: Sequences tr_B4R5K9_B4R5K9_DROSI_7240 and tr_A0A1W4VFS7_A0A1W4VFS7_DROFC_30025 are exactly identical! WARNING: Sequences tr_E2A405_E2A405_CAMFO_104421 and tr_E2BK35_E2BK35_HARSA_610380 are exactly identical! WARNING: Sequences tr_Q6PCA5_Q6PCA5_DANRE_7955 and tr_W5NHV5_W5NHV5_LEPOC_7918 are exactly identical! WARNING: Sequences tr_Q6PCA5_Q6PCA5_DANRE_7955 and tr_A0A0P7X0C2_A0A0P7X0C2_9TELE_113540 are exactly identical! WARNING: Sequences sp_O42406_SIX3_CHICK_9031 and tr_H9G823_H9G823_ANOCA_28377 are exactly identical! WARNING: Sequences sp_O42406_SIX3_CHICK_9031 and tr_A0A0Q3PGF8_A0A0Q3PGF8_AMAAE_12930 are exactly identical! WARNING: Sequences sp_O42406_SIX3_CHICK_9031 and tr_A0A1U7RB36_A0A1U7RB36_ALLSI_38654 are exactly identical! WARNING: Sequences sp_O42406_SIX3_CHICK_9031 and tr_A0A218UTF1_A0A218UTF1_9PASE_299123 are exactly identical! WARNING: Sequences sp_Q62231_SIX1_MOUSE_10090 and tr_G3IE65_G3IE65_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q62231_SIX1_MOUSE_10090 and tr_G3V970_G3V970_RAT_10116 are exactly identical! WARNING: Sequences sp_Q62231_SIX1_MOUSE_10090 and tr_A0A1U7Q8H1_A0A1U7Q8H1_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_H2QHU7_H2QHU7_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A0G2K2C0_A0A0G2K2C0_RAT_10116 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_H0XUM1_H0XUM1_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and sp_O95343_SIX3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A286ZW96_A0A286ZW96_PIG_9823 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_E1BMT1_E1BMT1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A0D9RLK6_A0A0D9RLK6_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A1S3FA15_A0A1S3FA15_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A2K5M5S4_A0A2K5M5S4_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A2U3W5M8_A0A2U3W5M8_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A2Y9KL34_A0A2Y9KL34_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A2Y9NDM0_A0A2Y9NDM0_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A2Y9FL85_A0A2Y9FL85_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q62233_SIX3_MOUSE_10090 and tr_A0A384ARX8_A0A384ARX8_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q9QZ28_SIX6_MOUSE_10090 and tr_D3ZCC7_D3ZCC7_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y4U9_M3Y4U9_MUSPF_9669 and tr_A0A2Y9IIV5_A0A2Y9IIV5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_E2R181_E2R181_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_F1S5K5_F1S5K5_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_D2GUA0_D2GUA0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_E1BJ27_E1BJ27_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_A0A2U3W5J3_A0A2U3W5J3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YKQ6_M3YKQ6_MUSPF_9669 and tr_A0A2Y9KSF8_A0A2Y9KSF8_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q95RW8_OPTIX_DROME_7227 and tr_B4HRI2_B4HRI2_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q95RW8_OPTIX_DROME_7227 and tr_A0A1W4WA96_A0A1W4WA96_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A3B3IIV2_A0A3B3IIV2_ORYLA_8090 and tr_A0A2I4CZC7_A0A2I4CZC7_9TELE_52670 are exactly identical! WARNING: Sequences tr_H2M3C2_H2M3C2_ORYLA_8090 and sp_O73916_SIX3_ORYLA_8090 are exactly identical! WARNING: Sequences tr_H2MM07_H2MM07_ORYLA_8090 and tr_I3KW48_I3KW48_ORENI_8128 are exactly identical! WARNING: Sequences tr_H2MM07_H2MM07_ORYLA_8090 and tr_G3P0L5_G3P0L5_GASAC_69293 are exactly identical! WARNING: Sequences tr_H2MM07_H2MM07_ORYLA_8090 and tr_A0A087XDK6_A0A087XDK6_POEFO_48698 are exactly identical! WARNING: Sequences tr_H2MM07_H2MM07_ORYLA_8090 and tr_A0A2I4BNM3_A0A2I4BNM3_9TELE_52670 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_H2NLF2_H2NLF2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_J9P3S7_J9P3S7_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_I3N0V4_I3N0V4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_G5C5H8_G5C5H8_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_M3XF50_M3XF50_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A2I3MLG5_A0A2I3MLG5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A091CTZ9_A0A091CTZ9_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A0D9RNX4_A0A0D9RNX4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A1S2ZH65_A0A1S2ZH65_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A2K5NJ34_A0A2K5NJ34_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RTX3_G1RTX3_NOMLE_61853 and tr_A0A2K5ZMB9_A0A2K5ZMB9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S4P9_G1S4P9_NOMLE_61853 and tr_H2QHU8_H2QHU8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S4P9_G1S4P9_NOMLE_61853 and sp_Q9NPC8_SIX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S4P9_G1S4P9_NOMLE_61853 and tr_F6Z031_F6Z031_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S4P9_G1S4P9_NOMLE_61853 and tr_A0A2R9BZP5_A0A2R9BZP5_PANPA_9597 are exactly identical! WARNING: Sequences sp_A1YER0_SIX1_GORGO_9595 and tr_H2Q8E8_H2Q8E8_PANTR_9598 are exactly identical! WARNING: Sequences sp_A1YER0_SIX1_GORGO_9595 and sp_Q15475_SIX1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A1YER0_SIX1_GORGO_9595 and tr_A0A2R9C4R6_A0A2R9C4R6_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1PN35_F1PN35_CANLF_9615 and tr_F7IFQ4_F7IFQ4_CALJA_9483 are exactly identical! WARNING: Sequences tr_F1PN35_F1PN35_CANLF_9615 and tr_G1L892_G1L892_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PN35_F1PN35_CANLF_9615 and tr_A0A1S2ZH54_A0A1S2ZH54_ERIEU_9365 are exactly identical! WARNING: Sequences tr_F1PN35_F1PN35_CANLF_9615 and tr_A0A2U3X147_A0A2U3X147_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PN35_F1PN35_CANLF_9615 and tr_A0A384CYH4_A0A384CYH4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2J8IMI8_A0A2J8IMI8_PANTR_9598 and tr_A0A2R8ZT65_A0A2R8ZT65_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q8E7_H2Q8E7_PANTR_9598 and sp_O95475_SIX6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q8E7_H2Q8E7_PANTR_9598 and tr_A0A2R9CLP7_A0A2R9CLP7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R5Z8_H2R5Z8_PANTR_9598 and sp_Q8N196_SIX5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7A7J5_K7A7J5_PANTR_9598 and tr_A0A2R9AGF8_A0A2R9AGF8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6PGM1_F6PGM1_MONDO_13616 and tr_G3WRH9_G3WRH9_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6W7Q8_F6W7Q8_HORSE_9796 and tr_A0A2Y9DAX2_A0A2Y9DAX2_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M4AYU4_M4AYU4_XIPMA_8083 and tr_I3IX46_I3IX46_ORENI_8128 are exactly identical! WARNING: Sequences tr_M4AYU4_M4AYU4_XIPMA_8083 and tr_A0A087XYP1_A0A087XYP1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NBK1_A0A158NBK1_ATTCE_12957 and tr_A0A195DRB2_A0A195DRB2_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NBK1_A0A158NBK1_ATTCE_12957 and tr_A0A195FE13_A0A195FE13_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NJ62_A0A158NJ62_ATTCE_12957 and tr_A0A195EXJ0_A0A195EXJ0_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3N8E1_I3N8E1_ICTTR_43179 and tr_A0A2Y9D7X8_A0A2Y9D7X8_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0X817_H0X817_OTOGA_30611 and tr_A0A2K6D3Z2_A0A2K6D3Z2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2T103_H2T103_TAKRU_31033 and tr_H3CPU1_H3CPU1_TETNG_99883 are exactly identical! WARNING: Sequences tr_F7D2Q7_F7D2Q7_MACMU_9544 and tr_G7PJJ0_G7PJJ0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7D2Q7_F7D2Q7_MACMU_9544 and tr_A0A2K6BS97_A0A2K6BS97_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q7PMT1_EXD_ANOGA_7165 and tr_A0A084W198_A0A084W198_ANOSI_74873 are exactly identical! WARNING: Sequences tr_H0Z093_H0Z093_TAEGU_59729 and tr_A0A218UT68_A0A218UT68_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZRY7_H0ZRY7_TAEGU_59729 and tr_A0A1V4KA27_A0A1V4KA27_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0ZRY7_H0ZRY7_TAEGU_59729 and tr_A0A218UYD0_A0A218UYD0_9PASE_299123 are exactly identical! WARNING: Sequences tr_G0NH25_G0NH25_CAEBE_135651 and tr_G0NH27_G0NH27_CAEBE_135651 are exactly identical! WARNING: Sequences tr_F7D0D8_F7D0D8_XENTR_8364 and tr_A0A151NXT6_A0A151NXT6_ALLMI_8496 are exactly identical! WARNING: Sequences tr_F7D0D8_F7D0D8_XENTR_8364 and tr_A0A1V4JJK3_A0A1V4JJK3_PATFA_372326 are exactly identical! WARNING: Sequences tr_F6YI63_F6YI63_CALJA_9483 and tr_A0A2I2U101_A0A2I2U101_FELCA_9685 are exactly identical! WARNING: Sequences tr_A8WY36_A8WY36_CAEBR_6238 and tr_A0A2G5TN77_A0A2G5TN77_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G7PAF4_G7PAF4_MACFA_9541 and tr_A0A2I3NCR1_A0A2I3NCR1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PAF4_G7PAF4_MACFA_9541 and tr_A0A0D9RNX9_A0A0D9RNX9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PAF4_G7PAF4_MACFA_9541 and tr_A0A2K5MTE1_A0A2K5MTE1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PAF4_G7PAF4_MACFA_9541 and tr_A0A2K6CPY7_A0A2K6CPY7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PAF4_G7PAF4_MACFA_9541 and tr_A0A2K5YDH8_A0A2K5YDH8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MM68_A0A096MM68_PAPAN_9555 and tr_A0A0D9S5T4_A0A0D9S5T4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NWW4_A0A096NWW4_PAPAN_9555 and tr_A0A0D9RLL8_A0A0D9RLL8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NWW4_A0A096NWW4_PAPAN_9555 and tr_A0A2K5KNN8_A0A2K5KNN8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NWW4_A0A096NWW4_PAPAN_9555 and tr_A0A2K6B329_A0A2K6B329_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NWW4_A0A096NWW4_PAPAN_9555 and tr_A0A2K6AKG2_A0A2K6AKG2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MXG2_A0A0A0MXG2_PAPAN_9555 and tr_A0A0D9S202_A0A0D9S202_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0A0MXG2_A0A0A0MXG2_PAPAN_9555 and tr_A0A2K5M9C0_A0A2K5M9C0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MXG2_A0A0A0MXG2_PAPAN_9555 and tr_A0A2K6BYS5_A0A2K6BYS5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MIH4_A0A2I3MIH4_PAPAN_9555 and tr_A0A0D9RNW7_A0A0D9RNW7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MIH4_A0A2I3MIH4_PAPAN_9555 and tr_A0A2K5NCV1_A0A2K5NCV1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MIH4_A0A2I3MIH4_PAPAN_9555 and tr_A0A2K5Y037_A0A2K5Y037_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0FJY8_A0A0K0FJY8_STRVS_75913 and tr_A0A0N5BL33_A0A0N5BL33_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0K0FU19_A0A0K0FU19_STRVS_75913 and tr_A0A0N5BAV6_A0A0N5BAV6_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A091EZY3_A0A091EZY3_CORBR_85066 and tr_A0A091UTS8_A0A091UTS8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EZY3_A0A091EZY3_CORBR_85066 and tr_A0A087QGS2_A0A087QGS2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EZY3_A0A091EZY3_CORBR_85066 and tr_A0A091J3U6_A0A091J3U6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0N0PDI6_A0A0N0PDI6_PAPMA_76193 and tr_A0A0N1IN86_A0A0N1IN86_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A194RF32_A0A194RF32_PAPMA_76193 and tr_A0A194QHW1_A0A194QHW1_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A091UWP1_A0A091UWP1_NIPNI_128390 and tr_A0A087QGS1_A0A087QGS1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UWP1_A0A091UWP1_NIPNI_128390 and tr_A0A091WCG1_A0A091WCG1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V1CZB9_A0A0V1CZB9_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V0WF88_A0A0V0WF88_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V0UZ88_A0A0V0UZ88_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V1KX02_A0A0V1KX02_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V0ZJ03_A0A0V0ZJ03_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RTL1_A0A0V0RTL1_9BILA_6336 and tr_A0A0V0TJS1_A0A0V0TJS1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V1CUN5_A0A0V1CUN5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V0WZ72_A0A0V0WZ72_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V0V254_A0A0V0V254_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V1L9P7_A0A0V1L9P7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V1A4X6_A0A0V1A4X6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V1PAE3_A0A0V1PAE3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RUE3_A0A0V0RUE3_9BILA_6336 and tr_A0A0V0U6G6_A0A0V0U6G6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MV78_A0A0V1MV78_9BILA_268474 and tr_A0A0V1I4G1_A0A0V1I4G1_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3Q650_A0A1S3Q650_SALSA_8030 and tr_A0A060VX27_A0A060VX27_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3Q7T6_A0A1S3Q7T6_SALSA_8030 and tr_A0A060VX95_A0A060VX95_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3R083_A0A1S3R083_SALSA_8030 and tr_A0A060VUY4_A0A060VUY4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_B5DG16_B5DG16_SALSA_8030 and tr_A0A060WWJ5_A0A060WWJ5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1U7R137_A0A1U7R137_MESAU_10036 and tr_A0A2K5ZD96_A0A2K5ZD96_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1U7R137_A0A1U7R137_MESAU_10036 and tr_A0A2U3YCA6_A0A2U3YCA6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A226ND16_A0A226ND16_CALSU_9009 and tr_A0A226PDZ7_A0A226PDZ7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226ND17_A0A226ND17_CALSU_9009 and tr_A0A226PD20_A0A226PD20_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0Q063_A0A2D0Q063_ICTPU_7998 and tr_A0A2D0Q1H0_A0A2D0Q1H0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V4B6_A0A2U3V4B6_TURTR_9739 and tr_A0A2Y9MZZ4_A0A2Y9MZZ4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V4B6_A0A2U3V4B6_TURTR_9739 and tr_A0A2Y9F9G2_A0A2Y9F9G2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V4B6_A0A2U3V4B6_TURTR_9739 and tr_A0A384B157_A0A384B157_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3WRL1_A0A2U3WRL1_ODORO_9708 and tr_A0A2U3XF53_A0A2U3XF53_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9N4X9_A0A2Y9N4X9_DELLE_9749 and tr_A0A2Y9FGA5_A0A2Y9FGA5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9N9E2_A0A2Y9N9E2_DELLE_9749 and tr_A0A2Y9SFT3_A0A2Y9SFT3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9P4H5_A0A2Y9P4H5_DELLE_9749 and tr_A0A2Y9EIR6_A0A2Y9EIR6_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 155 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.raxml.reduced.phy Alignment comprises 1 partitions and 284 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 284 Gaps: 22.39 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.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_040621/phylogeny-snakemake/results/Q15475/3_mltree/Q15475.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: -127339.219587 [00:00:00 -127339.219587] Initial branch length optimization [00:00:01 -86779.464545] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -86434.921013 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.202231,0.193590) (0.185185,0.295482) (0.291734,0.637819) (0.320850,2.244220) 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_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15475/4_raxmlng_ancestral/Q15475.raxml.log Analysis started: 19-Jun-2021 19:56:56 / finished: 19-Jun-2021 19:57:44 Elapsed time: 48.106 seconds