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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jul-2021 17:10:49 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/2_msa/P23258_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258 --seed 2 --threads 6 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/2_msa/P23258_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 427 sites WARNING: Sequences tr_V7BMV1_V7BMV1_PHAVU_3885 and tr_A0A0L9VL76_A0A0L9VL76_PHAAN_3914 are exactly identical! WARNING: Sequences tr_V7BMV1_V7BMV1_PHAVU_3885 and tr_A0A1S3TD02_A0A1S3TD02_VIGRR_3916 are exactly identical! WARNING: Sequences tr_B4Q911_B4Q911_DROSI_7240 and sp_P23257_TBG1_DROME_7227 are exactly identical! WARNING: Sequences tr_B4Q911_B4Q911_DROSI_7240 and tr_B4I2T2_B4I2T2_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4Q9H8_B4Q9H8_DROSI_7240 and sp_P42271_TBG2_DROME_7227 are exactly identical! WARNING: Sequences tr_B4Q9H8_B4Q9H8_DROSI_7240 and tr_B4I5S7_B4I5S7_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NU82_A0A1D5NU82_CHICK_9031 and tr_U3JD73_U3JD73_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5NU82_A0A1D5NU82_CHICK_9031 and tr_A0A0Q3PDS8_A0A0Q3PDS8_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A1D5NU82_A0A1D5NU82_CHICK_9031 and tr_A0A218UMV0_A0A218UMV0_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1D5NU82_A0A1D5NU82_CHICK_9031 and tr_A0A226MJ02_A0A226MJ02_CALSU_9009 are exactly identical! WARNING: Sequences sp_P83887_TBG1_MOUSE_10090 and tr_G3HLY0_G3HLY0_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P83887_TBG1_MOUSE_10090 and sp_P83888_TBG1_RAT_10116 are exactly identical! WARNING: Sequences sp_P83887_TBG1_MOUSE_10090 and tr_A0A1S3GYE4_A0A1S3GYE4_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_E2RD85_E2RD85_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_G3SLI6_G3SLI6_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_D2HIU4_D2HIU4_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_M3WFJ4_M3WFJ4_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_A0A2U3WNF9_A0A2U3WNF9_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_A0A2U3Y4I1_A0A2U3Y4I1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_A0A2Y9QGW7_A0A2Y9QGW7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_A0A2Y9K7T4_A0A2Y9K7T4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YFK7_M3YFK7_MUSPF_9669 and tr_A0A384CYG3_A0A384CYG3_URSMA_29073 are exactly identical! WARNING: Sequences tr_C5Z0K9_C5Z0K9_SORBI_4558 and tr_K3Y734_K3Y734_SETIT_4555 are exactly identical! WARNING: Sequences tr_C5Z0K9_C5Z0K9_SORBI_4558 and tr_A0A2T7E8H7_A0A2T7E8H7_9POAL_1504633 are exactly identical! WARNING: Sequences tr_G1RM10_G1RM10_NOMLE_61853 and tr_F7CYX8_F7CYX8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1PA44_G1PA44_MYOLU_59463 and tr_F6RCT5_F6RCT5_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PA44_G1PA44_MYOLU_59463 and tr_A0A287BRH5_A0A287BRH5_PIG_9823 are exactly identical! WARNING: Sequences tr_G1PA44_G1PA44_MYOLU_59463 and tr_A0A2Y9M8N1_A0A2Y9M8N1_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1PA44_G1PA44_MYOLU_59463 and tr_A0A2Y9EIE8_A0A2Y9EIE8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1PA44_G1PA44_MYOLU_59463 and tr_A0A383ZSD4_A0A383ZSD4_BALAS_310752 are exactly identical! WARNING: Sequences tr_J3K6Z9_J3K6Z9_COCIM_246410 and tr_A0A0J6Y5C8_A0A0J6Y5C8_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QCI4_B6QCI4_TALMQ_441960 and tr_B8M252_B8M252_TALSN_441959 are exactly identical! WARNING: Sequences tr_B2WIM4_B2WIM4_PYRTR_426418 and tr_M2SNZ4_M2SNZ4_COCSN_665912 are exactly identical! WARNING: Sequences tr_B2WIM4_B2WIM4_PYRTR_426418 and sp_P40633_TBG_COCH5_701091 are exactly identical! WARNING: Sequences tr_B2WIM4_B2WIM4_PYRTR_426418 and tr_W6XY45_W6XY45_COCCA_930089 are exactly identical! WARNING: Sequences tr_B2WIM4_B2WIM4_PYRTR_426418 and tr_W6Z723_W6Z723_COCMI_930090 are exactly identical! WARNING: Sequences tr_B2WIM4_B2WIM4_PYRTR_426418 and tr_A0A2W1EXA6_A0A2W1EXA6_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2I3RMD4_A0A2I3RMD4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and sp_Q9NRH3_TBG2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_F6TA66_F6TA66_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2I3MXI9_A0A2I3MXI9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A0D9S1M0_A0A0D9S1M0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A3Q0EGY3_A0A3Q0EGY3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2K5P246_A0A2K5P246_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2K6DEJ3_A0A2K6DEJ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2K5Z7N0_A0A2K5Z7N0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2Z9K2_A0A2I2Z9K2_GORGO_9595 and tr_A0A2R9BVC2_A0A2R9BVC2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2WW41_G2WW41_VERDV_498257 and tr_C9SB64_C9SB64_VERA1_526221 are exactly identical! WARNING: Sequences tr_G2WW41_G2WW41_VERDV_498257 and tr_A0A0G4NRE8_A0A0G4NRE8_9PEZI_100787 are exactly identical! WARNING: Sequences tr_C0NRF6_C0NRF6_AJECG_447093 and tr_C6HT81_C6HT81_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NRF6_C0NRF6_AJECG_447093 and tr_F0USZ5_F0USZ5_AJEC8_544711 are exactly identical! WARNING: Sequences sp_P53377_TBG_NEUCR_367110 and tr_G4UYS2_G4UYS2_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q29K32_Q29K32_DROPS_46245 and tr_B4GXF1_B4GXF1_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29KG7_Q29KG7_DROPS_46245 and tr_B4GSA4_B4GSA4_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8N4U1_B8N4U1_ASPFN_332952 and tr_Q2UCL4_Q2UCL4_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N4U1_B8N4U1_ASPFN_332952 and tr_A0A0F0IEN8_A0A0F0IEN8_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N4U1_B8N4U1_ASPFN_332952 and tr_A0A1S9DQA8_A0A1S9DQA8_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N4U1_B8N4U1_ASPFN_332952 and tr_A0A2G7FF12_A0A2G7FF12_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UKN2_A0A179UKN2_BLAGS_559298 and tr_C5GC93_C5GC93_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A125YV55_A0A125YV55_TOXGV_432359 and tr_A0A074T7B5_A0A074T7B5_HAMHA_99158 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_H0X1H2_H0X1H2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and sp_P23258_TBG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_A0A096P5U1_A0A096P5U1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_A0A0D9S1P2_A0A0D9S1P2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_A0A2K5LJL0_A0A2K5LJL0_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_A0A2K6AP10_A0A2K6AP10_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QD29_H2QD29_PANTR_9598 and tr_A0A2K5Z0E6_A0A2K5Z0E6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6QI90_F6QI90_HORSE_9796 and sp_Q0VCD2_TBG1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6QI90_F6QI90_HORSE_9796 and tr_L5JRU7_L5JRU7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F6QI90_F6QI90_HORSE_9796 and tr_A0A1S3WR84_A0A1S3WR84_ERIEU_9365 are exactly identical! WARNING: Sequences tr_F6QI90_F6QI90_HORSE_9796 and tr_A0A2Y9EIF8_A0A2Y9EIF8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6QI90_F6QI90_HORSE_9796 and tr_A0A383ZRM4_A0A383ZRM4_BALAS_310752 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_W7M5Z5_W7M5Z5_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_A0A0D2XN16_A0A0D2XN16_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_S0E6J2_S0E6J2_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_N4TGR0_N4TGR0_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_X0CI22_X0CI22_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_A0A2H3SMN3_A0A2H3SMN3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_A0A2H3H5H7_A0A2H3H5H7_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_A0A2K0W4J9_A0A2K0W4J9_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FLP1_F9FLP1_FUSOF_660025 and tr_A0A365MTV3_A0A365MTV3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9EZZ5_E9EZZ5_METRA_655844 and tr_A0A0D9PE46_A0A0D9PE46_METAN_1291518 are exactly identical! WARNING: Sequences tr_K4BK01_K4BK01_SOLLC_4081 and tr_M1B807_M1B807_SOLTU_4113 are exactly identical! WARNING: Sequences tr_A0A088ACY5_A0A088ACY5_APIME_7460 and tr_A0A2A3EDB3_A0A2A3EDB3_APICC_94128 are exactly identical! WARNING: Sequences tr_G9P6V2_G9P6V2_HYPAI_452589 and tr_A0A0W7VM60_A0A0W7VM60_9HYPO_398673 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_A0A0E0H9V1_A0A0E0H9V1_ORYNI_4536 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_B8AYG1_B8AYG1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_I1PSM3_I1PSM3_ORYGL_4538 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_A0A0E0PHS5_A0A0E0PHS5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_A0A0D3G3G1_A0A0D3G3G1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_A0A0D9ZUG4_A0A0D9ZUG4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and tr_A0A0D9WD18_A0A0D9WD18_9ORYZ_77586 are exactly identical! WARNING: Sequences tr_J3M448_J3M448_ORYBR_4533 and sp_O49068_TBG2_ORYSJ_39947 are exactly identical! WARNING: Sequences sp_P38557_TBG1_ARATH_3702 and tr_D7LSC6_D7LSC6_ARALL_81972 are exactly identical! WARNING: Sequences sp_P38557_TBG1_ARATH_3702 and tr_R0FN93_R0FN93_9BRAS_81985 are exactly identical! WARNING: Sequences tr_A2QRL5_A2QRL5_ASPNC_425011 and tr_G7XNK7_G7XNK7_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2QRL5_A2QRL5_ASPNC_425011 and tr_A0A1L9NPN0_A0A1L9NPN0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2QRL5_A2QRL5_ASPNC_425011 and tr_A0A1L9UP98_A0A1L9UP98_9EURO_767769 are exactly identical! WARNING: Sequences tr_A2QRL5_A2QRL5_ASPNC_425011 and tr_A0A317W3Z0_A0A317W3Z0_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2QRL5_A2QRL5_ASPNC_425011 and tr_A0A319AVD6_A0A319AVD6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A2K1IM18_A0A2K1IM18_PHYPA_3218 and tr_A0A2K1IXK0_A0A2K1IXK0_PHYPA_3218 are exactly identical! WARNING: Sequences tr_E5SFY5_E5SFY5_TRISP_6334 and tr_A0A0V0RVK6_A0A0V0RVK6_9BILA_6336 are exactly identical! WARNING: Sequences tr_F4X3G1_F4X3G1_ACREC_103372 and tr_A0A195DG20_A0A195DG20_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4X3G1_F4X3G1_ACREC_103372 and tr_A0A195BN07_A0A195BN07_9HYME_520822 are exactly identical! WARNING: Sequences tr_F9X1L1_F9X1L1_ZYMTI_336722 and tr_A0A0F4GAF0_A0A0F4GAF0_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9X1L1_F9X1L1_ZYMTI_336722 and tr_A0A1X7RIC5_A0A1X7RIC5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XUJ3_G2XUJ3_BOTF4_999810 and tr_M7U0P9_M7U0P9_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3QW35_E3QW35_COLGM_645133 and tr_A0A010RCZ0_A0A010RCZ0_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_E3QW35_E3QW35_COLGM_645133 and tr_A0A066XLV1_A0A066XLV1_COLSU_1173701 are exactly identical! WARNING: Sequences tr_E3QW35_E3QW35_COLGM_645133 and tr_A0A135US48_A0A135US48_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_E3QW35_E3QW35_COLGM_645133 and tr_A0A1G4BCL0_A0A1G4BCL0_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_G1LJ81_G1LJ81_AILME_9646 and tr_A0A341ZMI1_A0A341ZMI1_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1LJ81_G1LJ81_AILME_9646 and tr_A0A2U3WNG3_A0A2U3WNG3_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LJ81_G1LJ81_AILME_9646 and tr_A0A2U3Y4I0_A0A2U3Y4I0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LJ81_G1LJ81_AILME_9646 and tr_A0A384CYE8_A0A384CYE8_URSMA_29073 are exactly identical! WARNING: Sequences tr_G0RDS2_G0RDS2_HYPJQ_431241 and tr_A0A2T4CHG6_A0A2T4CHG6_TRILO_983965 are exactly identical! WARNING: Sequences tr_B3RKE6_B3RKE6_TRIAD_10228 and tr_A0A369S0F9_A0A369S0F9_9METZ_287889 are exactly identical! WARNING: Sequences tr_C4V916_C4V916_NOSCE_578460 and tr_A0A0F9WUS8_A0A0F9WUS8_9MICR_40302 are exactly identical! WARNING: Sequences tr_F2PXJ2_F2PXJ2_TRIEC_559882 and tr_A0A059IY36_A0A059IY36_9EURO_1215338 are exactly identical! WARNING: Sequences tr_D7UCL1_D7UCL1_VITVI_29760 and tr_A0A2C9WNY6_A0A2C9WNY6_MANES_3983 are exactly identical! WARNING: Sequences tr_L8FWK0_L8FWK0_PSED2_658429 and tr_A0A094DDT4_A0A094DDT4_9PEZI_1420910 are exactly identical! WARNING: Sequences tr_L8FWK0_L8FWK0_PSED2_658429 and tr_A0A1B8DZ64_A0A1B8DZ64_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_L8FWK0_L8FWK0_PSED2_658429 and tr_A0A1B8CKN4_A0A1B8CKN4_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A287EWW5_A0A287EWW5_HORVV_112509 and tr_M7Z165_M7Z165_TRIUA_4572 are exactly identical! WARNING: Sequences tr_A0A287EWW5_A0A287EWW5_HORVV_112509 and tr_A0A3B5XVX7_A0A3B5XVX7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A287EWW5_A0A287EWW5_HORVV_112509 and tr_W5A8H0_W5A8H0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M4CTS8_M4CTS8_BRARP_51351 and tr_A0A078FAD8_A0A078FAD8_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4CTS8_M4CTS8_BRARP_51351 and tr_A0A0D3DUW3_A0A0D3DUW3_BRAOL_109376 are exactly identical! WARNING: Sequences tr_R9NVK2_R9NVK2_PSEHS_1305764 and tr_V5EX86_V5EX86_KALBG_1365824 are exactly identical! WARNING: Sequences tr_R9NVK2_R9NVK2_PSEHS_1305764 and tr_A0A0F7S2A9_A0A0F7S2A9_9BASI_49012 are exactly identical! WARNING: Sequences tr_R0M462_R0M462_ANAPL_8839 and tr_A0A099ZCS8_A0A099ZCS8_TINGU_94827 are exactly identical! WARNING: Sequences tr_R0M462_R0M462_ANAPL_8839 and tr_A0A0A0A6H7_A0A0A0A6H7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_N1Q9N1_N1Q9N1_PSEFD_383855 and tr_A0A139GZG9_A0A139GZG9_9PEZI_321146 are exactly identical! WARNING: Sequences tr_U5HIF5_U5HIF5_USTV1_683840 and tr_A0A2X0N9E5_A0A2X0N9E5_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2QQA1_W2QQA1_PHYPN_761204 and tr_A0A0W8DKH5_A0A0W8DKH5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QQA1_W2QQA1_PHYPN_761204 and tr_W2JTT9_W2JTT9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A044SB54_A0A044SB54_ONCVO_6282 and tr_A0A182EFX2_A0A182EFX2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067HEK8_A0A067HEK8_CITSI_2711 and tr_V4TX58_V4TX58_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067HEK8_A0A067HEK8_CITSI_2711 and tr_A0A2H5PG94_A0A2H5PG94_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067JX25_A0A067JX25_JATCU_180498 and tr_A0A0A0L403_A0A0A0L403_CUCSA_3659 are exactly identical! WARNING: Sequences tr_A0A067JX25_A0A067JX25_JATCU_180498 and tr_A0A1S4DTR5_A0A1S4DTR5_CUCME_3656 are exactly identical! WARNING: Sequences tr_A0A067JX25_A0A067JX25_JATCU_180498 and tr_A0A2P5DDA6_A0A2P5DDA6_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A084QEK6_A0A084QEK6_STAC4_1283841 and tr_A0A084RED2_A0A084RED2_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A094F6S9_A0A094F6S9_9PEZI_1420912 and tr_A0A1B8GYC1_A0A1B8GYC1_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094F6S9_A0A094F6S9_9PEZI_1420912 and tr_A0A1B8F7D3_A0A1B8F7D3_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A0M8NXN8_A0A0M8NXN8_9EURO_229535 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A0G4P922_A0A0G4P922_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A101MET9_A0A101MET9_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A135LJE9_A0A135LJE9_PENPA_5078 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A1V6NG92_A0A1V6NG92_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A0A2JFQ7_A0A0A2JFQ7_PENEN_27334 and tr_A0A1V6R1I4_A0A1V6R1I4_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0D2SHT3_A0A0D2SHT3_GOSRA_29730 and tr_A0A1U8JXB0_A0A1U8JXB0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SHT3_A0A0D2SHT3_GOSRA_29730 and tr_A0A1U8L679_A0A1U8L679_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F9WWC8_A0A0F9WWC8_TRIHA_5544 and tr_A0A2T4ARG1_A0A2T4ARG1_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8XF55_A0A0F8XF55_9EURO_308745 and tr_A0A2T5M3K3_A0A2T5M3K3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0K0G0F8_A0A0K0G0F8_STRVS_75913 and tr_A0A0N5B2F7_A0A0N5B2F7_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0K8LM72_A0A0K8LM72_9EURO_91492 and tr_A0A0S7DYV4_A0A0S7DYV4_9EURO_293939 are exactly identical! WARNING: Sequences tr_A0A0K8LM72_A0A0K8LM72_9EURO_91492 and tr_A0A229X5A0_A0A229X5A0_9EURO_1245748 are exactly identical! WARNING: Sequences tr_A0A0K8LM72_A0A0K8LM72_9EURO_91492 and tr_A0A2I1C8R8_A0A2I1C8R8_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A0A0N0DDD5_A0A0N0DDD5_FUSLA_179993 and tr_A0A2T4GI85_A0A2T4GI85_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0A1MT90_A0A0A1MT90_9FUNG_58291 and tr_A0A2G4T1N8_A0A2G4T1N8_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1MT90_A0A0A1MT90_9FUNG_58291 and tr_A0A367K887_A0A367K887_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0D2EI97_A0A0D2EI97_9EURO_1442368 and tr_A0A0D2KIE4_A0A0D2KIE4_9EURO_1442371 are exactly identical! WARNING: Sequences tr_A0A0D2EI97_A0A0D2EI97_9EURO_1442368 and tr_A0A178Z530_A0A178Z530_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A091IN75_A0A091IN75_EGRGA_188379 and tr_A0A091UUA3_A0A091UUA3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IN75_A0A091IN75_EGRGA_188379 and tr_A0A087QJ97_A0A087QJ97_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IN75_A0A091IN75_EGRGA_188379 and tr_A0A091FNQ0_A0A091FNQ0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0N1IF23_A0A0N1IF23_PAPMA_76193 and tr_A0A194Q432_A0A194Q432_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0N1IF23_A0A0N1IF23_PAPMA_76193 and tr_A0A2A4JKN7_A0A2A4JKN7_HELVI_7102 are exactly identical! WARNING: Sequences tr_A0A0V1DHT3_A0A0V1DHT3_TRIBR_45882 and tr_A0A0V0WAM3_A0A0V0WAM3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DHT3_A0A0V1DHT3_TRIBR_45882 and tr_A0A0V1LU61_A0A0V1LU61_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DHT3_A0A0V1DHT3_TRIBR_45882 and tr_A0A0V0UGX3_A0A0V0UGX3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A165AKV3_A0A165AKV3_9HOMO_1314777 and tr_A0A166GU00_A0A166GU00_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A167J457_A0A167J457_9HYPO_1081107 and tr_A0A2N6NYM1_A0A2N6NYM1_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A1S4DDF2_A0A1S4DDF2_TOBAC_4097 and tr_A0A1U7XM15_A0A1U7XM15_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q9LEC3_Q9LEC3_TOBAC_4097 and tr_A0A1J6JCJ4_A0A1J6JCJ4_NICAT_49451 are exactly identical! WARNING: Sequences tr_Q9LEC3_Q9LEC3_TOBAC_4097 and tr_A0A1U7V5M8_A0A1U7V5M8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1E1LE48_A0A1E1LE48_9HELO_914237 and tr_A0A2V1BG33_A0A2V1BG33_9HELO_1485229 are exactly identical! WARNING: Sequences tr_A0A1R3S205_A0A1R3S205_ASPC5_602072 and tr_A0A317X861_A0A317X861_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A1V8U1S2_A0A1V8U1S2_9PEZI_1974281 and tr_A0A1V8TF91_A0A1V8TF91_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y2DWX3_A0A1Y2DWX3_9FUNG_1754190 and tr_A0A1Y1XCH9_A0A1Y1XCH9_9FUNG_1754192 are exactly identical! WARNING: Sequences tr_A0A251S6I6_A0A251S6I6_HELAN_4232 and tr_A0A251V137_A0A251V137_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A2H3EK41_A0A2H3EK41_9HELO_946125 and tr_A0A2H3EKY4_A0A2H3EKY4_9HELO_946125 are exactly identical! WARNING: Sequences tr_A0A2I1EAE5_A0A2I1EAE5_9GLOM_588596 and tr_U9TJI4_U9TJI4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2J6TS26_A0A2J6TS26_9HELO_1095630 and tr_A0A2J6S3C7_A0A2J6S3C7_9HELO_1149755 are exactly identical! WARNING: Sequences tr_A0A319C5A6_A0A319C5A6_9EURO_1448315 and tr_A0A2V5IUS2_A0A2V5IUS2_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319C5A6_A0A319C5A6_9EURO_1448315 and tr_A0A2V5HB40_A0A2V5HB40_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A319EXF2_A0A319EXF2_9EURO_1448318 and tr_A0A395GV81_A0A395GV81_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A369GJ72_A0A369GJ72_9HYPO_2039875 and tr_A0A367LFW8_A0A367LFW8_9HYPO_1330021 are exactly identical! WARNING: Duplicate sequences found: 189 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.reduced.phy Alignment comprises 1 partitions and 426 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 427 / 426 Gaps: 2.33 % Invariant sites: 0.70 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 213 / 17040 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -408119.280059] Initial branch length optimization [00:00:06 -344067.473212] Model parameter optimization (eps = 10.000000) [00:01:07 -342972.501705] AUTODETECT spr round 1 (radius: 5) [00:03:30 -231553.721922] AUTODETECT spr round 2 (radius: 10) [00:06:24 -174442.041565] AUTODETECT spr round 3 (radius: 15) [00:09:13 -146347.372444] AUTODETECT spr round 4 (radius: 20) [00:12:31 -130141.397750] AUTODETECT spr round 5 (radius: 25) [00:16:06 -128449.173098] SPR radius for FAST iterations: 25 (autodetect) [00:16:06 -128449.173098] Model parameter optimization (eps = 3.000000) [00:16:28 -128129.131094] FAST spr round 1 (radius: 25) [00:19:18 -106437.072539] FAST spr round 2 (radius: 25) [00:21:26 -105638.020245] FAST spr round 3 (radius: 25) [00:23:18 -105519.940940] FAST spr round 4 (radius: 25) [00:25:05 -105503.481256] FAST spr round 5 (radius: 25) [00:26:42 -105501.156664] FAST spr round 6 (radius: 25) [00:28:16 -105498.232471] FAST spr round 7 (radius: 25) [00:29:51 -105498.232469] Model parameter optimization (eps = 1.000000) [00:30:02 -105494.205988] SLOW spr round 1 (radius: 5) [00:32:12 -105474.417709] SLOW spr round 2 (radius: 5) [00:34:25 -105472.836537] SLOW spr round 3 (radius: 5) [00:36:34 -105472.519355] SLOW spr round 4 (radius: 5) [00:38:37 -105472.519138] SLOW spr round 5 (radius: 10) [00:40:45 -105472.517921] SLOW spr round 6 (radius: 15) [00:44:41 -105472.348928] SLOW spr round 7 (radius: 5) [00:47:23 -105472.347444] SLOW spr round 8 (radius: 10) [00:49:54 -105472.347430] SLOW spr round 9 (radius: 15) [00:53:24 -105472.347430] SLOW spr round 10 (radius: 20) [00:58:40 -105472.091815] SLOW spr round 11 (radius: 5) [01:01:25 -105472.091634] SLOW spr round 12 (radius: 10) [01:01:43] [worker #1] ML tree search #2, logLikelihood: -105477.879256 [01:04:04 -105470.681082] SLOW spr round 13 (radius: 5) [01:06:30 -105468.476648] SLOW spr round 14 (radius: 5) [01:08:40 -105468.476644] SLOW spr round 15 (radius: 10) [01:08:54] [worker #2] ML tree search #3, logLikelihood: -105462.908360 [01:10:46 -105468.476643] SLOW spr round 16 (radius: 15) [01:14:27 -105467.176427] SLOW spr round 17 (radius: 5) [01:17:04 -105467.176418] SLOW spr round 18 (radius: 10) [01:19:37 -105465.769487] SLOW spr round 19 (radius: 5) [01:22:01 -105465.769352] SLOW spr round 20 (radius: 10) [01:24:20 -105465.769352] SLOW spr round 21 (radius: 15) [01:27:49 -105465.769352] SLOW spr round 22 (radius: 20) [01:32:57 -105465.769352] SLOW spr round 23 (radius: 25) [01:39:30 -105465.769352] Model parameter optimization (eps = 0.100000) [01:39:38] [worker #0] ML tree search #1, logLikelihood: -105465.487342 [01:39:38 -404159.753828] Initial branch length optimization [01:39:46 -339151.067986] Model parameter optimization (eps = 10.000000) [01:40:54 -338087.439809] AUTODETECT spr round 1 (radius: 5) [01:43:19 -230487.779914] AUTODETECT spr round 2 (radius: 10) [01:45:53 -177080.189843] AUTODETECT spr round 3 (radius: 15) [01:48:31 -136938.145540] AUTODETECT spr round 4 (radius: 20) [01:51:28 -126387.006447] AUTODETECT spr round 5 (radius: 25) [01:55:21 -122391.112934] SPR radius for FAST iterations: 25 (autodetect) [01:55:21 -122391.112934] Model parameter optimization (eps = 3.000000) [01:55:46 -121996.236650] FAST spr round 1 (radius: 25) [01:58:45 -106224.945698] FAST spr round 2 (radius: 25) [02:00:51 -105879.617286] FAST spr round 3 (radius: 25) [02:02:38 -105840.666343] FAST spr round 4 (radius: 25) [02:04:23 -105830.527172] FAST spr round 5 (radius: 25) [02:06:00 -105830.527108] Model parameter optimization (eps = 1.000000) [02:06:17 -105811.226109] SLOW spr round 1 (radius: 5) [02:08:32 -105792.045571] SLOW spr round 2 (radius: 5) [02:09:10] [worker #1] ML tree search #5, logLikelihood: -105463.226253 [02:10:42 -105792.044302] SLOW spr round 3 (radius: 10) [02:12:57 -105788.516205] SLOW spr round 4 (radius: 5) [02:15:41 -105785.280337] SLOW spr round 5 (radius: 5) [02:18:05 -105785.280220] SLOW spr round 6 (radius: 10) [02:20:20 -105785.063528] SLOW spr round 7 (radius: 5) [02:22:57 -105785.063417] SLOW spr round 8 (radius: 10) [02:25:26 -105785.063414] SLOW spr round 9 (radius: 15) [02:29:02 -105784.020734] SLOW spr round 10 (radius: 5) [02:31:50 -105784.020622] SLOW spr round 11 (radius: 10) [02:34:30 -105782.610837] SLOW spr round 12 (radius: 5) [02:37:05 -105782.610830] SLOW spr round 13 (radius: 10) [02:39:32 -105782.610825] SLOW spr round 14 (radius: 15) [02:43:08 -105782.610795] SLOW spr round 15 (radius: 20) [02:48:20 -105782.610795] SLOW spr round 16 (radius: 25) [02:54:36] [worker #2] ML tree search #6, logLikelihood: -105444.477816 [02:55:04 -105486.170409] SLOW spr round 17 (radius: 5) [02:57:59 -105484.146471] SLOW spr round 18 (radius: 5) [03:00:26 -105484.144914] SLOW spr round 19 (radius: 10) [03:02:46 -105484.144822] SLOW spr round 20 (radius: 15) [03:06:12 -105484.144818] SLOW spr round 21 (radius: 20) [03:11:06 -105476.010949] SLOW spr round 22 (radius: 5) [03:13:52 -105472.578319] SLOW spr round 23 (radius: 5) [03:16:16 -105468.957822] SLOW spr round 24 (radius: 5) [03:18:25 -105467.937516] SLOW spr round 25 (radius: 5) [03:20:28 -105467.937499] SLOW spr round 26 (radius: 10) [03:22:32 -105467.394231] SLOW spr round 27 (radius: 5) [03:23:30] [worker #1] ML tree search #8, logLikelihood: -105460.220371 [03:25:04 -105457.372538] SLOW spr round 28 (radius: 5) [03:27:17 -105457.372273] SLOW spr round 29 (radius: 10) [03:29:25 -105457.372270] SLOW spr round 30 (radius: 15) [03:32:54 -105457.372270] SLOW spr round 31 (radius: 20) [03:37:46 -105457.372270] SLOW spr round 32 (radius: 25) [03:44:06 -105457.372270] Model parameter optimization (eps = 0.100000) [03:44:14] [worker #0] ML tree search #4, logLikelihood: -105456.486008 [03:44:14 -411847.027644] Initial branch length optimization [03:44:20 -347188.908574] Model parameter optimization (eps = 10.000000) [03:45:23 -346102.219707] AUTODETECT spr round 1 (radius: 5) [03:47:54 -231088.327595] AUTODETECT spr round 2 (radius: 10) [03:51:00 -176609.752670] AUTODETECT spr round 3 (radius: 15) [03:53:47 -149925.280635] AUTODETECT spr round 4 (radius: 20) [03:57:10 -133030.418113] AUTODETECT spr round 5 (radius: 25) [04:01:01 -130094.597340] SPR radius for FAST iterations: 25 (autodetect) [04:01:01 -130094.597340] Model parameter optimization (eps = 3.000000) [04:01:24 -129752.272316] FAST spr round 1 (radius: 25) [04:04:34 -107529.334701] FAST spr round 2 (radius: 25) [04:06:45 -105558.313094] FAST spr round 3 (radius: 25) [04:08:38 -105520.451453] FAST spr round 4 (radius: 25) [04:10:21 -105515.296024] FAST spr round 5 (radius: 25) [04:11:59 -105515.294767] Model parameter optimization (eps = 1.000000) [04:12:13 -105508.289976] SLOW spr round 1 (radius: 5) [04:14:28 -105467.690111] SLOW spr round 2 (radius: 5) [04:16:40 -105466.884267] SLOW spr round 3 (radius: 5) [04:18:50 -105465.808707] SLOW spr round 4 (radius: 5) [04:20:36] [worker #2] ML tree search #9, logLikelihood: -105502.873612 [04:20:59 -105465.808062] SLOW spr round 5 (radius: 10) [04:23:10 -105465.807804] SLOW spr round 6 (radius: 15) [04:27:03 -105464.822603] SLOW spr round 7 (radius: 5) [04:29:51 -105464.822571] SLOW spr round 8 (radius: 10) [04:30:58] [worker #1] ML tree search #11, logLikelihood: -105477.281043 [04:32:31 -105464.822562] SLOW spr round 9 (radius: 15) [04:36:09 -105464.764983] SLOW spr round 10 (radius: 20) [04:41:51 -105464.764593] SLOW spr round 11 (radius: 25) [04:49:07 -105464.764586] Model parameter optimization (eps = 0.100000) [04:49:15] [worker #0] ML tree search #7, logLikelihood: -105464.698274 [04:49:15 -408835.566288] Initial branch length optimization [04:49:22 -345153.137688] Model parameter optimization (eps = 10.000000) [04:50:26 -343993.473703] AUTODETECT spr round 1 (radius: 5) [04:53:00 -231117.932584] AUTODETECT spr round 2 (radius: 10) [04:56:00 -177879.973357] AUTODETECT spr round 3 (radius: 15) [04:58:39 -147370.470214] AUTODETECT spr round 4 (radius: 20) [05:01:47 -133022.825439] AUTODETECT spr round 5 (radius: 25) [05:05:17 -128646.428182] SPR radius for FAST iterations: 25 (autodetect) [05:05:17 -128646.428182] Model parameter optimization (eps = 3.000000) [05:05:38 -128330.157420] FAST spr round 1 (radius: 25) [05:08:55 -106479.906198] FAST spr round 2 (radius: 25) [05:11:07 -105590.831914] FAST spr round 3 (radius: 25) [05:13:05 -105508.373344] FAST spr round 4 (radius: 25) [05:14:48 -105504.465896] FAST spr round 5 (radius: 25) [05:16:24 -105502.910831] FAST spr round 6 (radius: 25) [05:17:58 -105502.910828] Model parameter optimization (eps = 1.000000) [05:18:13 -105496.811655] SLOW spr round 1 (radius: 5) [05:20:26 -105474.632111] SLOW spr round 2 (radius: 5) [05:22:38 -105473.836748] SLOW spr round 3 (radius: 5) [05:24:47 -105473.836108] SLOW spr round 4 (radius: 10) [05:26:56 -105473.836071] SLOW spr round 5 (radius: 15) [05:30:39 -105472.061272] SLOW spr round 6 (radius: 5) [05:33:27 -105472.061057] SLOW spr round 7 (radius: 10) [05:36:02 -105470.873976] SLOW spr round 8 (radius: 5) [05:38:38 -105470.873879] SLOW spr round 9 (radius: 10) [05:39:46] [worker #1] ML tree search #14, logLikelihood: -105476.542678 [05:40:42] [worker #2] ML tree search #12, logLikelihood: -105481.165695 [05:41:02 -105470.873866] SLOW spr round 10 (radius: 15) [05:44:29 -105470.820870] SLOW spr round 11 (radius: 20) [05:49:13 -105470.820456] SLOW spr round 12 (radius: 25) [05:55:26 -105470.820450] Model parameter optimization (eps = 0.100000) [05:55:31] [worker #0] ML tree search #10, logLikelihood: -105470.814606 [05:55:31 -409551.959865] Initial branch length optimization [05:55:36 -345840.365379] Model parameter optimization (eps = 10.000000) [05:56:46 -344770.676195] AUTODETECT spr round 1 (radius: 5) [05:59:22 -227344.791678] AUTODETECT spr round 2 (radius: 10) [06:02:22 -166768.150321] AUTODETECT spr round 3 (radius: 15) [06:05:09 -146937.593174] AUTODETECT spr round 4 (radius: 20) [06:08:58 -127131.003526] AUTODETECT spr round 5 (radius: 25) [06:12:37 -125723.270955] SPR radius for FAST iterations: 25 (autodetect) [06:12:37 -125723.270955] Model parameter optimization (eps = 3.000000) [06:13:04 -125345.873341] FAST spr round 1 (radius: 25) [06:16:05 -106314.935403] FAST spr round 2 (radius: 25) [06:18:26 -105605.606067] FAST spr round 3 (radius: 25) [06:20:26 -105528.183616] FAST spr round 4 (radius: 25) [06:22:17 -105513.903572] FAST spr round 5 (radius: 25) [06:24:01 -105511.769151] FAST spr round 6 (radius: 25) [06:25:38 -105511.768549] Model parameter optimization (eps = 1.000000) [06:25:54 -105496.768046] SLOW spr round 1 (radius: 5) [06:28:06 -105480.250884] SLOW spr round 2 (radius: 5) [06:30:20 -105477.702759] SLOW spr round 3 (radius: 5) [06:32:34 -105473.903391] SLOW spr round 4 (radius: 5) [06:34:42 -105473.902955] SLOW spr round 5 (radius: 10) [06:36:54 -105473.850164] SLOW spr round 6 (radius: 15) [06:40:43 -105473.849751] SLOW spr round 7 (radius: 20) [06:44:53] [worker #2] ML tree search #15, logLikelihood: -105453.375745 [06:45:41 -105473.849745] SLOW spr round 8 (radius: 25) [06:52:23 -105473.849745] Model parameter optimization (eps = 0.100000) [06:52:28] [worker #0] ML tree search #13, logLikelihood: -105473.836695 [06:52:28 -408563.017725] Initial branch length optimization [06:52:35 -343604.335391] Model parameter optimization (eps = 10.000000) [06:53:35 -342466.051798] AUTODETECT spr round 1 (radius: 5) [06:56:07 -228930.222487] AUTODETECT spr round 2 (radius: 10) [06:57:46] [worker #1] ML tree search #17, logLikelihood: -105474.174174 [06:59:12 -174123.088048] AUTODETECT spr round 3 (radius: 15) [07:02:04 -147159.344177] AUTODETECT spr round 4 (radius: 20) [07:05:30 -133052.616155] AUTODETECT spr round 5 (radius: 25) [07:09:33 -127804.242964] SPR radius for FAST iterations: 25 (autodetect) [07:09:33 -127804.242964] Model parameter optimization (eps = 3.000000) [07:09:56 -127488.511113] FAST spr round 1 (radius: 25) [07:13:00 -106326.210064] FAST spr round 2 (radius: 25) [07:15:13 -105680.068710] FAST spr round 3 (radius: 25) [07:17:10 -105520.373068] FAST spr round 4 (radius: 25) [07:18:56 -105512.708997] FAST spr round 5 (radius: 25) [07:20:34 -105512.708518] Model parameter optimization (eps = 1.000000) [07:20:47 -105508.915901] SLOW spr round 1 (radius: 5) [07:23:02 -105489.125877] SLOW spr round 2 (radius: 5) [07:25:16 -105478.199463] SLOW spr round 3 (radius: 5) [07:27:34 -105476.125266] SLOW spr round 4 (radius: 5) [07:29:48 -105476.125197] SLOW spr round 5 (radius: 10) [07:32:03 -105474.764309] SLOW spr round 6 (radius: 5) [07:34:50 -105470.990624] SLOW spr round 7 (radius: 5) [07:37:17 -105470.990606] SLOW spr round 8 (radius: 10) [07:39:33 -105470.990606] SLOW spr round 9 (radius: 15) [07:43:10 -105470.932587] SLOW spr round 10 (radius: 20) [07:48:07 -105470.932200] SLOW spr round 11 (radius: 25) [07:54:36 -105470.932195] Model parameter optimization (eps = 0.100000) [07:54:44] [worker #0] ML tree search #16, logLikelihood: -105470.719013 [07:54:44 -405442.040476] Initial branch length optimization [07:54:52 -342311.583944] Model parameter optimization (eps = 10.000000) [07:56:22 -341152.691045] AUTODETECT spr round 1 (radius: 5) [07:59:00 -229942.392665] AUTODETECT spr round 2 (radius: 10) [08:01:49 -172774.132911] AUTODETECT spr round 3 (radius: 15) [08:04:40 -144750.880856] AUTODETECT spr round 4 (radius: 20) [08:08:02 -133051.926228] AUTODETECT spr round 5 (radius: 25) [08:10:57] [worker #2] ML tree search #18, logLikelihood: -105461.622826 [08:12:14 -129494.441897] SPR radius for FAST iterations: 25 (autodetect) [08:12:14 -129494.441897] Model parameter optimization (eps = 3.000000) [08:12:46 -129180.652789] FAST spr round 1 (radius: 25) [08:15:51 -108607.969423] FAST spr round 2 (radius: 25) [08:18:02 -105915.862729] FAST spr round 3 (radius: 25) [08:20:02 -105541.196620] FAST spr round 4 (radius: 25) [08:21:49 -105482.020252] FAST spr round 5 (radius: 25) [08:23:27 -105479.396418] FAST spr round 6 (radius: 25) [08:24:08] [worker #1] ML tree search #20, logLikelihood: -105463.788271 [08:25:01 -105479.396380] Model parameter optimization (eps = 1.000000) [08:25:13 -105474.123124] SLOW spr round 1 (radius: 5) [08:27:22 -105453.546052] SLOW spr round 2 (radius: 5) [08:29:32 -105451.630182] SLOW spr round 3 (radius: 5) [08:31:38 -105451.630092] SLOW spr round 4 (radius: 10) [08:33:51 -105451.629777] SLOW spr round 5 (radius: 15) [08:38:01 -105450.880943] SLOW spr round 6 (radius: 5) [08:40:51 -105450.660753] SLOW spr round 7 (radius: 5) [08:43:16 -105450.660738] SLOW spr round 8 (radius: 10) [08:45:34 -105450.607712] SLOW spr round 9 (radius: 15) [08:49:12 -105450.607301] SLOW spr round 10 (radius: 20) [08:54:17 -105450.607296] SLOW spr round 11 (radius: 25) [09:01:05 -105450.607296] Model parameter optimization (eps = 0.100000) [09:01:10] [worker #0] ML tree search #19, logLikelihood: -105450.572117 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.305578,0.518952) (0.296315,0.669777) (0.271695,1.057816) (0.126411,2.812650) 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 Final LogLikelihood: -105444.477816 AIC score: 214898.955632 / AICc score: 8258958.955632 / BIC score: 223032.807578 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=427). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 229 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P23258/3_mltree/P23258.raxml.log Analysis started: 02-Jul-2021 17:10:49 / finished: 03-Jul-2021 02:12:00 Elapsed time: 32470.496 seconds Consumed energy: 2353.576 Wh (= 12 km in an electric car, or 59 km with an e-scooter!)