RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 14:16:34 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/2_msa/P78368_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/3_mltree/P78368.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805394 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/2_msa/P78368_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 415 sites WARNING: Sequences tr_B4QX55_B4QX55_DROSI_7240 and tr_B4IBY2_B4IBY2_DROSE_7238 are exactly identical! WARNING: Sequences tr_B6H617_B6H617_PENRW_500485 and tr_A0A1V6Y3V8_A0A1V6Y3V8_PENNA_60175 are exactly identical! WARNING: Sequences tr_E3RQ19_E3RQ19_PYRTT_861557 and tr_B2W1T6_B2W1T6_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RQ19_E3RQ19_PYRTT_861557 and tr_A0A2W1D0C1_A0A2W1D0C1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_A0A2I2ZVN9_A0A2I2ZVN9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_A0A2I3T0G2_A0A2I3T0G2_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_G8F3J7_G8F3J7_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_A0A2I3LHC6_A0A2I3LHC6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_A0A2K5YF96_A0A2K5YF96_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3H6C4_A0A2I3H6C4_NOMLE_61853 and tr_A0A2R9BFG2_A0A2R9BFG2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_G3RIR2_G3RIR2_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2I3TNT3_A0A2I3TNT3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_F7H415_F7H415_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_U3E6K8_U3E6K8_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2I3M5Y1_A0A2I3M5Y1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2K5MPG6_A0A2K5MPG6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2K6C1A0_A0A2K6C1A0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2K6ACR3_A0A2K6ACR3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HFC2_A0A2I3HFC2_NOMLE_61853 and tr_A0A2R8ZYA3_A0A2R8ZYA3_PANPA_9597 are exactly identical! WARNING: Sequences tr_B6Q861_B6Q861_TALMQ_441960 and tr_A0A093VWS5_A0A093VWS5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2J8R3W5_A0A2J8R3W5_PONAB_9601 and tr_K7D4Y0_K7D4Y0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NNG8_H2NNG8_PONAB_9601 and sp_Q9HCP0_KC1G1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NNG8_H2NNG8_PONAB_9601 and tr_A0A0D9RJ80_A0A0D9RJ80_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3JAA9_G3JAA9_CORMM_983644 and tr_A0A168FLZ5_A0A168FLZ5_CORDF_1081108 are exactly identical! WARNING: Sequences tr_V5IKR9_V5IKR9_NEUCR_367110 and tr_G4UYX8_G4UYX8_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N4N0_B8N4N0_ASPFN_332952 and tr_Q2UMB2_Q2UMB2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N4N0_B8N4N0_ASPFN_332952 and tr_A0A1S9DP32_A0A1S9DP32_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UEW2_A0A179UEW2_BLAGS_559298 and tr_C5GE84_C5GE84_AJEDR_559297 are exactly identical! WARNING: Sequences tr_Q5KI40_Q5KI40_CRYNJ_214684 and tr_E6R4K5_E6R4K5_CRYGW_367775 are exactly identical! WARNING: Sequences tr_Q5KI40_Q5KI40_CRYNJ_214684 and tr_A0A095D0P0_A0A095D0P0_CRYGR_294750 are exactly identical! WARNING: Sequences tr_F7CH57_F7CH57_HORSE_9796 and tr_A0A2U4BTB6_A0A2U4BTB6_TURTR_9739 are exactly identical! WARNING: Sequences tr_F7CH57_F7CH57_HORSE_9796 and tr_A0A2Y9PM79_A0A2Y9PM79_DELLE_9749 are exactly identical! WARNING: Sequences tr_F7CH57_F7CH57_HORSE_9796 and tr_A0A2Y9S6B5_A0A2Y9S6B5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F7CH57_F7CH57_HORSE_9796 and tr_A0A384AMH6_A0A384AMH6_BALAS_310752 are exactly identical! WARNING: Sequences tr_W5PU37_W5PU37_SHEEP_9940 and tr_A7MB90_A7MB90_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_W7LP22_W7LP22_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_S0E1T5_S0E1T5_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_N4TY83_N4TY83_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_X0CJS7_X0CJS7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_A0A2H3SMD4_A0A2H3SMD4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_A0A2H3GXP1_A0A2H3GXP1_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9F7C0_F9F7C0_FUSOF_660025 and tr_A0A365MTM8_A0A365MTM8_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9ESH5_E9ESH5_METRA_655844 and tr_A0A0B4I738_A0A0B4I738_METMF_1276143 are exactly identical! WARNING: Sequences tr_I3LZV3_I3LZV3_ICTTR_43179 and tr_F1RKN8_F1RKN8_PIG_9823 are exactly identical! WARNING: Sequences tr_I3LZV3_I3LZV3_ICTTR_43179 and tr_A0A2Y9JLW1_A0A2Y9JLW1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A1DM86_A1DM86_NEOFI_331117 and tr_A0A0S7DLT0_A0A0S7DLT0_9EURO_293939 are exactly identical! WARNING: Sequences tr_A1DM86_A1DM86_NEOFI_331117 and tr_A0A2I1CDJ5_A0A2I1CDJ5_9EURO_1392255 are exactly identical! WARNING: Sequences tr_F7HDF6_F7HDF6_MACMU_9544 and tr_A0A2K6E8G9_A0A2K6E8G9_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9EP27_H9EP27_MACMU_9544 and tr_A0A0A0MV40_A0A0A0MV40_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9EP27_H9EP27_MACMU_9544 and tr_A0A0D9RHJ4_A0A0D9RHJ4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9EP27_H9EP27_MACMU_9544 and tr_A0A2K5M1W7_A0A2K5M1W7_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9EP27_H9EP27_MACMU_9544 and tr_A0A2K6CUQ7_A0A2K6CUQ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_E6QY49_E6QY49_CRYGW_367775 and tr_A0A095C739_A0A095C739_CRYGR_294750 are exactly identical! WARNING: Sequences tr_G0P4W8_G0P4W8_CAEBE_135651 and tr_A0A1I7TTJ8_A0A1I7TTJ8_9PELO_1561998 are exactly identical! WARNING: Sequences tr_G2YDU1_G2YDU1_BOTF4_999810 and tr_M7UD83_M7UD83_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3MG61_E3MG61_CAERE_31234 and tr_A0A261AV56_A0A261AV56_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3QBH0_E3QBH0_COLGM_645133 and tr_A0A066XCI0_A0A066XCI0_COLSU_1173701 are exactly identical! WARNING: Sequences tr_E3QBH0_E3QBH0_COLGM_645133 and tr_A0A161WEM7_A0A161WEM7_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_F2SYB8_F2SYB8_TRIRC_559305 and tr_A0A178F515_A0A178F515_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G1L0F1_G1L0F1_AILME_9646 and tr_A0A1S3WH66_A0A1S3WH66_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1L0F1_G1L0F1_AILME_9646 and tr_A0A3Q0DMD8_A0A3Q0DMD8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1L0F1_G1L0F1_AILME_9646 and tr_A0A2U3ZI02_A0A2U3ZI02_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1L0F1_G1L0F1_AILME_9646 and tr_A0A2U3YI57_A0A2U3YI57_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G0RMC0_G0RMC0_HYPJQ_431241 and tr_A0A2T4CA19_A0A2T4CA19_TRILO_983965 are exactly identical! WARNING: Sequences tr_G0RMC0_G0RMC0_HYPJQ_431241 and tr_A0A2T4BK34_A0A2T4BK34_9HYPO_58853 are exactly identical! WARNING: Sequences tr_G3YEI5_G3YEI5_ASPNA_380704 and tr_A0A319AMF9_A0A319AMF9_9EURO_1450533 are exactly identical! WARNING: Sequences tr_L0PH29_L0PH29_PNEJ8_1209962 and tr_A0A0W4ZUC9_A0A0W4ZUC9_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L8G2W6_L8G2W6_PSED2_658429 and tr_A0A094GH94_A0A094GH94_9PEZI_1420912 are exactly identical! WARNING: Sequences tr_L8G2W6_L8G2W6_PSED2_658429 and tr_A0A1B8F2C2_A0A1B8F2C2_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_L2GGR9_L2GGR9_COLFN_1213859 and tr_T0KRK5_T0KRK5_COLGC_1237896 are exactly identical! WARNING: Sequences tr_U3KH39_U3KH39_FICAL_59894 and tr_A0A218US70_A0A218US70_9PASE_299123 are exactly identical! WARNING: Sequences tr_M2RYE7_M2RYE7_COCSN_665912 and tr_M2VDE9_M2VDE9_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2RYE7_M2RYE7_COCSN_665912 and tr_W6Y1J5_W6Y1J5_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2RYE7_M2RYE7_COCSN_665912 and tr_W6ZT21_W6ZT21_COCMI_930090 are exactly identical! WARNING: Sequences tr_W9XBH1_W9XBH1_9EURO_1182542 and tr_W9YI29_W9YI29_9EURO_1182541 are exactly identical! WARNING: Sequences tr_A0A017ST55_A0A017ST55_9EURO_1388766 and tr_A0A1L9V3E9_A0A1L9V3E9_ASPGL_1160497 are exactly identical! WARNING: Sequences tr_A0A010Q902_A0A010Q902_9PEZI_1445577 and tr_A0A135V0J9_A0A135V0J9_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A044TY51_A0A044TY51_ONCVO_6282 and tr_A0A182EBL8_A0A182EBL8_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A074XTC8_A0A074XTC8_9PEZI_1043004 and tr_A0A074YNW9_A0A074YNW9_9PEZI_1043005 are exactly identical! WARNING: Sequences tr_A0A074XTC8_A0A074XTC8_9PEZI_1043004 and tr_A0A074VMG2_A0A074VMG2_9PEZI_1043003 are exactly identical! WARNING: Sequences tr_A0A074XTC8_A0A074XTC8_9PEZI_1043004 and tr_A0A074XFW1_A0A074XFW1_AURPU_1043002 are exactly identical! WARNING: Sequences tr_A0A094GIZ6_A0A094GIZ6_9PEZI_1420912 and tr_A0A1B8GM98_A0A1B8GM98_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A060SKD9_A0A060SKD9_PYCCI_5643 and tr_A0A1Y2IZ69_A0A1Y2IZ69_PYCCO_1353009 are exactly identical! WARNING: Sequences tr_A0A0A2VG87_A0A0A2VG87_BEABA_1245745 and tr_A0A167KVI3_A0A167KVI3_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_A0A0A2VG87_A0A0A2VG87_BEABA_1245745 and tr_A0A2N6NIZ0_A0A2N6NIZ0_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0D2PFM1_A0A0D2PFM1_GOSRA_29730 and tr_A0A1U8LJ72_A0A1U8LJ72_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F0IBM5_A0A0F0IBM5_ASPPU_1403190 and tr_A0A0L1ISA5_A0A0L1ISA5_ASPNO_1509407 are exactly identical! WARNING: Sequences tr_A0A0F0IBM5_A0A0F0IBM5_ASPPU_1403190 and tr_A0A1F7ZR88_A0A1F7ZR88_9EURO_109264 are exactly identical! WARNING: Sequences tr_A0A0F0IBM5_A0A0F0IBM5_ASPPU_1403190 and tr_A0A2G7FMC6_A0A2G7FMC6_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A2A9PNZ9_A0A2A9PNZ9_9HYPO_268505 and tr_A0A369H0E6_A0A369H0E6_9HYPO_2039874 are exactly identical! WARNING: Sequences tr_A0A2A9PNZ9_A0A2A9PNZ9_9HYPO_268505 and tr_A0A367L4F9_A0A367L4F9_9HYPO_1330021 are exactly identical! WARNING: Sequences tr_A0A0A1MK67_A0A0A1MK67_9FUNG_58291 and tr_A0A367J630_A0A367J630_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1NFL4_A0A0A1NFL4_9FUNG_58291 and tr_A0A0A1P8G3_A0A0A1P8G3_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0A1NFL4_A0A0A1NFL4_9FUNG_58291 and tr_A0A367JJ08_A0A367JJ08_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1P349_A0A0A1P349_9FUNG_58291 and tr_A0A2G4SNN7_A0A2G4SNN7_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A091UUJ0_A0A091UUJ0_NIPNI_128390 and tr_A0A087RCW5_A0A087RCW5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UUJ0_A0A091UUJ0_NIPNI_128390 and tr_A0A091G8R2_A0A091G8R2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UUJ0_A0A091UUJ0_NIPNI_128390 and tr_A0A091I788_A0A091I788_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0G4PLV2_A0A0G4PLV2_PENCA_1429867 and tr_A0A1V6R8G8_A0A1V6R8G8_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0V1CPP7_A0A0V1CPP7_TRIBR_45882 and tr_A0A0V0WUJ2_A0A0V0WUJ2_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CPP7_A0A0V1CPP7_TRIBR_45882 and tr_A0A0V0VAW8_A0A0V0VAW8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CPP7_A0A0V1CPP7_TRIBR_45882 and tr_A0A0V1L828_A0A0V1L828_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CPP7_A0A0V1CPP7_TRIBR_45882 and tr_A0A0V1PCF0_A0A0V1PCF0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CPP7_A0A0V1CPP7_TRIBR_45882 and tr_A0A0V0U1R2_A0A0V0U1R2_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0YAJ9_A0A0V0YAJ9_TRIPS_6337 and tr_A0A0V1N2H2_A0A0V1N2H2_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0W7VQD9_A0A0W7VQD9_9HYPO_398673 and tr_A0A2T3Z284_A0A2T3Z284_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_A0A117E1S4_A0A117E1S4_ASPNG_5061 and tr_A0A1L9NMJ2_A0A1L9NMJ2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A117E1S4_A0A117E1S4_ASPNG_5061 and tr_A0A317UKM8_A0A317UKM8_9EURO_1448314 are exactly identical! WARNING: Sequences tr_I1S050_I1S050_GIBZE_229533 and tr_A0A2T4GIG2_A0A2T4GIG2_FUSCU_5516 are exactly identical! WARNING: Sequences tr_I1S050_I1S050_GIBZE_229533 and tr_A0A2L2TMV9_A0A2L2TMV9_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A164S0S1_A0A164S0S1_9HOMO_1314777 and tr_A0A166CZ38_A0A166CZ38_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3T3L3_A0A1S3T3L3_SALSA_8030 and tr_A0A060X257_A0A060X257_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B9IRB6_A0A1B9IRB6_9TREE_1331196 and tr_A0A1B9GDN1_A0A1B9GDN1_9TREE_1296100 are exactly identical! WARNING: Sequences tr_A0A1V8USI6_A0A1V8USI6_9PEZI_1974281 and tr_A0A1V8SVD1_A0A1V8SVD1_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Z5SRE0_A0A1Z5SRE0_HORWE_1157616 and tr_A0A1Z5T768_A0A1Z5T768_HORWE_1157616 are exactly identical! WARNING: Sequences tr_A0A2H3E8V1_A0A2H3E8V1_ARMGA_47427 and tr_A0A284QVS7_A0A284QVS7_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3BXG1_A0A2H3BXG1_9AGAR_1076256 and tr_A0A284QUB5_A0A284QUB5_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3IKD9_A0A2H3IKD9_9EURO_290292 and tr_A0A364KKT2_A0A364KKT2_9EURO_1196081 are exactly identical! WARNING: Sequences tr_A0A2D0QY87_A0A2D0QY87_ICTPU_7998 and tr_W5UJQ3_W5UJQ3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SVN8_A0A2D0SVN8_ICTPU_7998 and tr_W5UEL4_W5UEL4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2N5S9A2_A0A2N5S9A2_9BASI_200324 and tr_A0A2N5W5D2_A0A2N5W5D2_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2S7QM46_A0A2S7QM46_9HELO_2070414 and tr_A0A2S7QVB9_A0A2S7QVB9_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2V5INY0_A0A2V5INY0_9EURO_1450541 and tr_A0A2V5IHI7_A0A2V5IHI7_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 123 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.reduced.phy Alignment comprises 1 partitions and 415 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 415 Gaps: 14.01 % Invariant sites: 2.17 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/3_mltree/P78368.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320 [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: -78265.577873 [00:00:00 -78265.577873] Initial branch length optimization [00:00:01 -76783.151954] Model parameter optimization (eps = 0.100000) [00:00:33] Tree #1, final logLikelihood: -76619.969805 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.257569,0.209935) (0.295651,0.359163) (0.218533,0.967640) (0.228247,2.752628) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P78368/4_raxmlng_ancestral/P78368.raxml.log Analysis started: 04-Jun-2021 14:16:34 / finished: 04-Jun-2021 14:17:11 Elapsed time: 37.294 seconds