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 02:41:40 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/2_msa/O60663_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/3_mltree/O60663.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/4_raxmlng_ancestral/O60663 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677300 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/O60663/2_msa/O60663_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 402 sites WARNING: Sequences tr_B4Q9G3_B4Q9G3_DROSI_7240 and tr_B4N183_B4N183_DROWI_7260 are exactly identical! WARNING: Sequences tr_B4QR86_B4QR86_DROSI_7240 and tr_B4HFL2_B4HFL2_DROSE_7238 are exactly identical! WARNING: Sequences tr_E1BQX0_E1BQX0_CHICK_9031 and tr_U3JZ92_U3JZ92_FICAL_59894 are exactly identical! WARNING: Sequences sp_P53412_LHX3_CHICK_9031 and tr_A0A226NIN6_A0A226NIN6_CALSU_9009 are exactly identical! WARNING: Sequences sp_P53412_LHX3_CHICK_9031 and tr_A0A226P8J5_A0A226P8J5_COLVI_9014 are exactly identical! WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_M3YR06_M3YR06_MUSPF_9669 are exactly identical! WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_I3NEG6_I3NEG6_ICTTR_43179 are exactly identical! WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_F6VZX1_F6VZX1_MACMU_9544 are exactly identical! WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_A0A2R8PA11_A0A2R8PA11_CALJA_9483 are exactly identical! WARNING: Sequences sp_O88609_LMX1B_MOUSE_10090 and tr_A0A286ZUN2_A0A286ZUN2_PIG_9823 are exactly identical! WARNING: Sequences sp_P61375_LHX5_MOUSE_10090 and sp_P61376_LHX5_RAT_10116 are exactly identical! WARNING: Sequences sp_P61375_LHX5_MOUSE_10090 and tr_A0A1U7R1F6_A0A1U7R1F6_MESAU_10036 are exactly identical! WARNING: Sequences sp_P63006_LHX1_MOUSE_10090 and sp_P63007_LHX1_RAT_10116 are exactly identical! WARNING: Sequences sp_P63006_LHX1_MOUSE_10090 and tr_G3W9N9_G3W9N9_SARHA_9305 are exactly identical! WARNING: Sequences sp_P63006_LHX1_MOUSE_10090 and sp_P63008_LHX1_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9CXV0_ISL2_MOUSE_10090 and tr_A0A1U7Q5B2_A0A1U7Q5B2_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XUB0_M3XUB0_MUSPF_9669 and tr_L5KVQ5_L5KVQ5_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3XUB0_M3XUB0_MUSPF_9669 and tr_A0A2U3WN78_A0A2U3WN78_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XUB0_M3XUB0_MUSPF_9669 and tr_A0A2U3YET5_A0A2U3YET5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XUB0_M3XUB0_MUSPF_9669 and tr_A0A2Y9KPF7_A0A2Y9KPF7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XXF7_M3XXF7_MUSPF_9669 and tr_F1PDJ1_F1PDJ1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_G1PQP4_G1PQP4_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_G3QJR1_G3QJR1_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_H2NTG1_H2NTG1_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_E2RMA8_E2RMA8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and sp_Q5IS44_LHX1_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_H0VUK6_H0VUK6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and sp_P48742_LHX1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_G3SY40_G3SY40_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_F6UGX4_F6UGX4_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A286ZJJ7_A0A286ZJJ7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A7Z015_A7Z015_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2I2V4T1_A0A2I2V4T1_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A096P515_A0A096P515_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A0D9R170_A0A0D9R170_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A1S2ZC01_A0A1S2ZC01_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A1S3EWA0_A0A1S3EWA0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2K5MHK7_A0A2K5MHK7_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2K6CQU0_A0A2K6CQU0_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2K5YD72_A0A2K5YD72_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2R9C5I6_A0A2R9C5I6_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2U3UYH4_A0A2U3UYH4_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2U3VR91_A0A2U3VR91_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2U3XMR7_A0A2U3XMR7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2Y9DNC8_A0A2Y9DNC8_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2Y9LSS0_A0A2Y9LSS0_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A2Y9EDY4_A0A2Y9EDY4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YUD9_M3YUD9_MUSPF_9669 and tr_A0A384ASD1_A0A384ASD1_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_F6X948_F6X948_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_I3M715_I3M715_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_M3VU13_M3VU13_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_A0A1S2ZWV5_A0A1S2ZWV5_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_A0A2U3WYC0_A0A2U3WYC0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z0X5_M3Z0X5_MUSPF_9669 and tr_A0A2Y9K292_A0A2Y9K292_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8IRC7_AWH_DROME_7227 and tr_B4HTV0_B4HTV0_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_G3SJ98_G3SJ98_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A2I3S5M9_A0A2I3S5M9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A288CFZ4_A0A288CFZ4_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_G1L9U3_G1L9U3_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A2R9BAU6_A0A2R9BAU6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A2U3ZS73_A0A2U3ZS73_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3GL84_A0A2I3GL84_NOMLE_61853 and tr_A0A384C241_A0A384C241_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_F7C7F3_F7C7F3_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_W5Q9X8_W5Q9X8_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_F1MFM7_F1MFM7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_A0A096MXS7_A0A096MXS7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_A0A0D9RIY0_A0A0D9RIY0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_A0A2K5P7Q5_A0A2K5P7Q5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_A0A2K6DHK8_A0A2K6DHK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1NUE8_G1NUE8_MYOLU_59463 and tr_A0A2Y9M4I7_A0A2Y9M4I7_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A2J8LM37_A0A2J8LM37_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and sp_Q8TE12_LMX1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_F7HWH3_F7HWH3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_G7NU26_G7NU26_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A096NWR5_A0A096NWR5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A2K5KHP5_A0A2K5KHP5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A2K6BHU9_A0A2K6BHU9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A2K5ZET9_A0A2K5ZET9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QL82_G3QL82_GORGO_9595 and tr_A0A2R9ASW8_A0A2R9ASW8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R2B6_G3R2B6_GORGO_9595 and tr_G7P7H4_G7P7H4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R2B6_G3R2B6_GORGO_9595 and tr_A0A3Q0E4L3_A0A3Q0E4L3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3R4V4_G3R4V4_GORGO_9595 and tr_H2Q6Y3_H2Q6Y3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R4V4_G3R4V4_GORGO_9595 and sp_Q9H2C1_LHX5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R4V4_G3R4V4_GORGO_9595 and tr_A0A2R9B0Q4_A0A2R9B0Q4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RTM0_G3RTM0_GORGO_9595 and tr_H2N4H9_H2N4H9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RTM0_G3RTM0_GORGO_9595 and tr_H2Q0P9_H2Q0P9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RTM0_G3RTM0_GORGO_9595 and sp_Q969G2_LHX4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RTM0_G3RTM0_GORGO_9595 and tr_A0A2R9CST7_A0A2R9CST7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_H2NNW1_H2NNW1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_H2Q9V1_H2Q9V1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and sp_Q96A47_ISL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_F7DL07_F7DL07_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_A0A0D9RQB4_A0A0D9RQB4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_A0A2K5M8G6_A0A2K5M8G6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SG14_G3SG14_GORGO_9595 and tr_A0A2K6B824_A0A2K6B824_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2N712_H2N712_PONAB_9601 and sp_Q68G74_LHX8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NIS2_H2NIS2_PONAB_9601 and tr_F7I4X9_F7I4X9_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NIS2_H2NIS2_PONAB_9601 and tr_A0A096N1Z4_A0A096N1Z4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NIS2_H2NIS2_PONAB_9601 and tr_A0A0D9S494_A0A0D9S494_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NIS2_H2NIS2_PONAB_9601 and tr_A0A2K5MAM7_A0A2K5MAM7_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NIS2_H2NIS2_PONAB_9601 and tr_A0A2K6B8G3_A0A2K6B8G3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PTF0_H2PTF0_PONAB_9601 and tr_G3TF87_G3TF87_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H2PTF0_H2PTF0_PONAB_9601 and tr_A0A1S3FJM1_A0A1S3FJM1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1U4X0_G1U4X0_RABIT_9986 and tr_A0A1S3WHS2_A0A1S3WHS2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1U4X0_G1U4X0_RABIT_9986 and tr_A0A2U3XQF1_A0A2U3XQF1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_Q2M074_Q2M074_DROPS_46245 and tr_B4GS09_B4GS09_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M0Q7_Q2M0Q7_DROPS_46245 and tr_B4GR87_B4GR87_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_H0WI04_H0WI04_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and sp_O60663_LMX1B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_D2H3X4_D2H3X4_AILME_9646 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2I2V362_A0A2I2V362_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A0D9RMI6_A0A0D9RMI6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2K6C4K9_A0A2K6C4K9_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2Y9NL89_A0A2Y9NL89_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2QXW6_H2QXW6_PANTR_9598 and tr_A0A2Y9T224_A0A2Y9T224_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6QG57_F6QG57_MONDO_13616 and tr_K7FA63_K7FA63_PELSI_13735 are exactly identical! WARNING: Sequences tr_F6QG57_F6QG57_MONDO_13616 and tr_A0A1U7RC74_A0A1U7RC74_ALLSI_38654 are exactly identical! WARNING: Sequences tr_W5NTQ5_W5NTQ5_SHEEP_9940 and tr_A0A287BE81_A0A287BE81_PIG_9823 are exactly identical! WARNING: Sequences tr_W5NTQ5_W5NTQ5_SHEEP_9940 and tr_E1BM60_E1BM60_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5NTQ5_W5NTQ5_SHEEP_9940 and tr_A0A2U4CN35_A0A2U4CN35_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5NTQ5_W5NTQ5_SHEEP_9940 and tr_A0A2Y9F0Z8_A0A2Y9F0Z8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5NTQ5_W5NTQ5_SHEEP_9940 and tr_A0A383ZEI7_A0A383ZEI7_BALAS_310752 are exactly identical! WARNING: Sequences tr_W5PEU1_W5PEU1_SHEEP_9940 and tr_H0XVQ4_H0XVQ4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M4ARX6_M4ARX6_XIPMA_8083 and tr_A0A087YEM1_A0A087YEM1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NQJ4_A0A158NQJ4_ATTCE_12957 and tr_F4WKB4_F4WKB4_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NQJ4_A0A158NQJ4_ATTCE_12957 and tr_A0A151XAX7_A0A151XAX7_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NQJ4_A0A158NQJ4_ATTCE_12957 and tr_A0A195DHV1_A0A195DHV1_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NRM9_A0A158NRM9_ATTCE_12957 and tr_F4X3D8_F4X3D8_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NRM9_A0A158NRM9_ATTCE_12957 and tr_A0A195DG31_A0A195DG31_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NRM9_A0A158NRM9_ATTCE_12957 and tr_A0A195BN66_A0A195BN66_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NRM9_A0A158NRM9_ATTCE_12957 and tr_A0A195EX03_A0A195EX03_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3MZ08_I3MZ08_ICTTR_43179 and tr_A0A1U7U8S0_A0A1U7U8S0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H0WMY0_H0WMY0_OTOGA_30611 and tr_G3TEI7_G3TEI7_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H0WMY0_H0WMY0_OTOGA_30611 and tr_F1RKD0_F1RKD0_PIG_9823 are exactly identical! WARNING: Sequences tr_H0WMY0_H0WMY0_OTOGA_30611 and tr_A0A2Y9LAJ1_A0A2Y9LAJ1_DELLE_9749 are exactly identical! WARNING: Sequences tr_H0YVX4_H0YVX4_TAEGU_59729 and tr_U3K9T9_U3K9T9_FICAL_59894 are exactly identical! WARNING: Sequences tr_E3MG77_E3MG77_CAERE_31234 and tr_A0A261AT74_A0A261AT74_9PELO_1503980 are exactly identical! WARNING: Sequences tr_B4MD89_B4MD89_DROVI_7244 and tr_B4L3K6_B4L3K6_DROMO_7230 are exactly identical! WARNING: Sequences tr_Q16S23_Q16S23_AEDAE_7159 and tr_Q173L2_Q173L2_AEDAE_7159 are exactly identical! WARNING: Sequences tr_G1LJ50_G1LJ50_AILME_9646 and tr_A0A384BP82_A0A384BP82_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A091D1I7_A0A091D1I7_FUKDA_885580 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A0D9RVX7_A0A0D9RVX7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A1S2ZGD2_A0A1S2ZGD2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A1S3FDG9_A0A1S3FDG9_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A1U7QNL2_A0A1U7QNL2_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and sp_P61373_ISL1_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2K5MRF3_A0A2K5MRF3_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2K6DK81_A0A2K6DK81_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2K5XS53_A0A2K5XS53_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2R9B1B8_A0A2R9B1B8_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2U3V9B1_A0A2U3V9B1_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2U3WPE0_A0A2U3WPE0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2U3XJV0_A0A2U3XJV0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2Y9DSS7_A0A2Y9DSS7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2Y9IL80_A0A2Y9IL80_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A2Y9EWU9_A0A2Y9EWU9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A384C8I4_A0A384C8I4_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3WF59_M3WF59_FELCA_9685 and tr_A0A384B7J6_A0A384B7J6_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3JRU9_U3JRU9_FICAL_59894 and tr_A0A1V4K1Z6_A0A1V4K1Z6_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3JRU9_U3JRU9_FICAL_59894 and tr_A0A218UV54_A0A218UV54_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A087XSG2_A0A087XSG2_POEFO_48698 and tr_A0A087XTM0_A0A087XTM0_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2I3LDJ2_A0A2I3LDJ2_PAPAN_9555 and tr_A0A2K5MVV3_A0A2K5MVV3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LDJ2_A0A2I3LDJ2_PAPAN_9555 and tr_A0A2K6AYA2_A0A2K6AYA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091F9K6_A0A091F9K6_CORBR_85066 and tr_A0A093QTZ0_A0A093QTZ0_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JEH4_A0A091JEH4_EGRGA_188379 and tr_A0A087R3M5_A0A087R3M5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JEH4_A0A091JEH4_EGRGA_188379 and tr_A0A093HUM0_A0A093HUM0_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JEH4_A0A091JEH4_EGRGA_188379 and tr_A0A091H8L4_A0A091H8L4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JEH4_A0A091JEH4_EGRGA_188379 and tr_A0A0A0AX62_A0A0A0AX62_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JMZ3_A0A091JMZ3_EGRGA_188379 and tr_A0A091UYX2_A0A091UYX2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JMZ3_A0A091JMZ3_EGRGA_188379 and tr_A0A087QVJ1_A0A087QVJ1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JMZ3_A0A091JMZ3_EGRGA_188379 and tr_A0A091G1Y1_A0A091G1Y1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JMZ3_A0A091JMZ3_EGRGA_188379 and tr_A0A093GN63_A0A093GN63_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091JMZ3_A0A091JMZ3_EGRGA_188379 and tr_A0A091J150_A0A091J150_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1CMQ5_A0A0V1CMQ5_TRIBR_45882 and tr_A0A0V0TWA8_A0A0V0TWA8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WYT9_A0A0V0WYT9_9BILA_92179 and tr_A0A0V0VC06_A0A0V0VC06_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WYT9_A0A0V0WYT9_9BILA_92179 and tr_A0A0V1L3N7_A0A0V1L3N7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WYT9_A0A0V0WYT9_9BILA_92179 and tr_A0A0V0TV71_A0A0V0TV71_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X786_A0A0V0X786_9BILA_92179 and tr_A0A0V1L3A2_A0A0V1L3A2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X786_A0A0V0X786_9BILA_92179 and tr_A0A0V1P7D4_A0A0V1P7D4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3LSM5_A0A1S3LSM5_SALSA_8030 and tr_A0A060WLE7_A0A060WLE7_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3M6U0_A0A1S3M6U0_SALSA_8030 and tr_B5XFD3_B5XFD3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3PBF2_A0A1S3PBF2_SALSA_8030 and tr_A0A060WE19_A0A060WE19_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PVG5_A0A1S3PVG5_SALSA_8030 and tr_A0A060Y988_A0A060Y988_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3T1R2_A0A1S3T1R2_SALSA_8030 and tr_A0A060Y7L0_A0A060Y7L0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1U7Q2H5_A0A1U7Q2H5_MESAU_10036 and sp_Q04650_LMX1A_MESAU_10036 are exactly identical! WARNING: Duplicate sequences found: 185 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/O60663/4_raxmlng_ancestral/O60663.raxml.reduced.phy Alignment comprises 1 partitions and 402 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 402 Gaps: 29.85 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/4_raxmlng_ancestral/O60663.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/O60663/3_mltree/O60663.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 101 / 8080 [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: -106286.985733 [00:00:00 -106286.985733] Initial branch length optimization [00:00:01 -92308.204697] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -92159.255868 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.189740,0.159160) (0.113713,0.363835) (0.280946,0.842935) (0.415602,1.664116) 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/O60663/4_raxmlng_ancestral/O60663.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/4_raxmlng_ancestral/O60663.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/4_raxmlng_ancestral/O60663.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60663/4_raxmlng_ancestral/O60663.raxml.log Analysis started: 03-Jun-2021 02:41:40 / finished: 03-Jun-2021 02:42:37 Elapsed time: 57.327 seconds Consumed energy: 3.407 Wh