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 06-Jul-2021 02:57:34 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/2_msa/Q13627_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/2_msa/Q13627_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 350 sites WARNING: Sequences tr_B4R6Q2_B4R6Q2_DROSI_7240 and sp_P49657_MNB_DROME_7227 are exactly identical! WARNING: Sequences tr_D1L3Y5_D1L3Y5_DANRE_7955 and tr_W5MB76_W5MB76_LEPOC_7918 are exactly identical! WARNING: Sequences tr_D1L3Y5_D1L3Y5_DANRE_7955 and tr_A0A1S3NBF7_A0A1S3NBF7_SALSA_8030 are exactly identical! WARNING: Sequences tr_D1L3Y5_D1L3Y5_DANRE_7955 and tr_A0A1S3RXL0_A0A1S3RXL0_SALSA_8030 are exactly identical! WARNING: Sequences tr_D1L3Y5_D1L3Y5_DANRE_7955 and tr_A0A2D0PQU8_A0A2D0PQU8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and sp_Q61214_DYR1A_MOUSE_10090 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_G1NVL6_G1NVL6_MYOLU_59463 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_G1SPQ6_G1SPQ6_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_H2QL08_H2QL08_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and sp_Q63470_DYR1A_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and sp_Q13627_DYR1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_F7FBT7_F7FBT7_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_G3SME5_G3SME5_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A096NJ33_A0A096NJ33_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A0D9R801_A0A0D9R801_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A1S3G2G8_A0A1S3G2G8_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A1U8C7W5_A0A1U8C7W5_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A226NLQ6_A0A226NLQ6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2K5P1R8_A0A2K5P1R8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2K6B4V6_A0A2K6B4V6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2K5ZRQ1_A0A2K5ZRQ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2R9AN66_A0A2R9AN66_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2U4AB97_A0A2U4AB97_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2Y9QLT4_A0A2Y9QLT4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2Y9LNG7_A0A2Y9LNG7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A1D5NW90_A0A1D5NW90_CHICK_9031 and tr_A0A2Y9EWY3_A0A2Y9EWY3_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q9Z188_DYR1B_MOUSE_10090 and tr_A0A287D5B9_A0A287D5B9_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q9Z188_DYR1B_MOUSE_10090 and tr_H0VGB8_H0VGB8_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YAN5_M3YAN5_MUSPF_9669 and tr_A0A2Y9KJR0_A0A2Y9KJR0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z1Z3_M3Z1Z3_MUSPF_9669 and tr_E2RG45_E2RG45_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z1Z3_M3Z1Z3_MUSPF_9669 and tr_L5L580_L5L580_PTEAL_9402 are exactly identical! WARNING: Sequences tr_A0A3B3I4M3_A0A3B3I4M3_ORYLA_8090 and tr_M3ZHM0_M3ZHM0_XIPMA_8083 are exactly identical! WARNING: Sequences tr_A0A3B3I4M3_A0A3B3I4M3_ORYLA_8090 and tr_A0A096MGE3_A0A096MGE3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B3I4M3_A0A3B3I4M3_ORYLA_8090 and tr_A0A2I4D8D7_A0A2I4D8D7_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A0E1RV60_A0A0E1RV60_COCIM_246410 and tr_E9DCT7_E9DCT7_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1RV60_A0A0E1RV60_COCIM_246410 and tr_A0A0J7B8G7_A0A0J7B8G7_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WIP7_B2WIP7_PYRTR_426418 and tr_A0A2W1EVT9_A0A2W1EVT9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I2YPW0_A0A2I2YPW0_GORGO_9595 and tr_A0A2J8SDP1_A0A2J8SDP1_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YPW0_A0A2I2YPW0_GORGO_9595 and tr_F7GIB1_F7GIB1_MACMU_9544 are exactly identical! WARNING: Sequences tr_C0NXA2_C0NXA2_AJECG_447093 and tr_C6HI82_C6HI82_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NXA2_C0NXA2_AJECG_447093 and tr_F0UHG7_F0UHG7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_G1NNY8_G1NNY8_MELGA_9103 and tr_I3MR02_I3MR02_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1NNY8_G1NNY8_MELGA_9103 and tr_I3L9V1_I3L9V1_PIG_9823 are exactly identical! WARNING: Sequences tr_G1KII2_G1KII2_ANOCA_28377 and tr_F6WIF6_F6WIF6_ORNAN_9258 are exactly identical! WARNING: Sequences tr_G1KII2_G1KII2_ANOCA_28377 and tr_F6S561_F6S561_MONDO_13616 are exactly identical! WARNING: Sequences tr_G1KII2_G1KII2_ANOCA_28377 and tr_G3WFE4_G3WFE4_SARHA_9305 are exactly identical! WARNING: Sequences tr_Q7SBT7_Q7SBT7_NEUCR_367110 and tr_F7W136_F7W136_SORMK_771870 are exactly identical! WARNING: Sequences tr_Q7SBT7_Q7SBT7_NEUCR_367110 and tr_G4UNS8_G4UNS8_NEUT9_510952 are exactly identical! WARNING: Sequences tr_V5IPB8_V5IPB8_NEUCR_367110 and tr_G4UGS8_G4UGS8_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q29KB0_Q29KB0_DROPS_46245 and tr_B4GX60_B4GX60_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NCT9_B8NCT9_ASPFN_332952 and tr_A0A0L1JGY5_A0A0L1JGY5_ASPNO_1509407 are exactly identical! WARNING: Sequences tr_B8NCT9_B8NCT9_ASPFN_332952 and tr_A0A1F7ZX75_A0A1F7ZX75_9EURO_109264 are exactly identical! WARNING: Sequences tr_B8NCT9_B8NCT9_ASPFN_332952 and tr_A0A1S9DCV5_A0A1S9DCV5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NFB9_B8NFB9_ASPFN_332952 and tr_A0A1S9DBG3_A0A1S9DBG3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179V1H8_A0A179V1H8_BLAGS_559298 and tr_C5GS77_C5GS77_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179V1H8_A0A179V1H8_BLAGS_559298 and tr_A0A1J9PUR4_A0A1J9PUR4_9EURO_1658174 are exactly identical! WARNING: Sequences tr_F1P9L4_F1P9L4_CANLF_9615 and tr_G1MIS8_G1MIS8_AILME_9646 are exactly identical! WARNING: Sequences tr_F1P9L4_F1P9L4_CANLF_9615 and tr_A0A337RZ15_A0A337RZ15_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1P9L4_F1P9L4_CANLF_9615 and tr_A0A2U3WXB3_A0A2U3WXB3_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1P9L4_F1P9L4_CANLF_9615 and tr_A0A2U3YTL6_A0A2U3YTL6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1P9L4_F1P9L4_CANLF_9615 and tr_A0A384CZA5_A0A384CZA5_URSMA_29073 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and sp_Q9Y463_DYR1B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and tr_A0A0A0MUR9_A0A0A0MUR9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and tr_A0A2K5MZG1_A0A2K5MZG1_CERAT_9531 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and tr_A0A2K6E229_A0A2K6E229_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and tr_A0A2K5YAA4_A0A2K5YAA4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_W7MGT5_W7MGT5_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_A0A0D2XZP9_A0A0D2XZP9_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_S0E909_S0E909_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_N4USN2_N4USN2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_X0DKF1_X0DKF1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_A0A2H3TRJ8_A0A2H3TRJ8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_A0A2H3H385_A0A2H3H385_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_A0A2K0WI53_A0A2K0WI53_GIBNY_42673 are exactly identical! WARNING: Sequences tr_Q4W9S9_Q4W9S9_ASPFU_330879 and tr_A1D9P2_A1D9P2_NEOFI_331117 are exactly identical! WARNING: Sequences tr_Q4W9S9_Q4W9S9_ASPFU_330879 and tr_A0A0K8LPJ1_A0A0K8LPJ1_9EURO_91492 are exactly identical! WARNING: Sequences tr_Q4W9S9_Q4W9S9_ASPFU_330879 and tr_A0A0S7DXP0_A0A0S7DXP0_9EURO_293939 are exactly identical! WARNING: Sequences tr_M3ZN20_M3ZN20_XIPMA_8083 and tr_A0A087X2V9_A0A087X2V9_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088AN80_A0A088AN80_APIME_7460 and tr_A0A0L7QWE1_A0A0L7QWE1_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A158NGB0_A0A158NGB0_ATTCE_12957 and tr_A0A195ET37_A0A195ET37_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NGB0_A0A158NGB0_ATTCE_12957 and tr_A0A151IIQ0_A0A151IIQ0_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A158NXL8_A0A158NXL8_ATTCE_12957 and tr_A0A151I2M2_A0A151I2M2_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3JYW1_I3JYW1_ORENI_8128 and tr_H2SWR8_H2SWR8_TAKRU_31033 are exactly identical! WARNING: Sequences tr_I3JYW1_I3JYW1_ORENI_8128 and tr_G3P875_G3P875_GASAC_69293 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_I3LSF5_I3LSF5_PIG_9823 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_A2VDT2_A2VDT2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_A0A2U3YIB3_A0A2U3YIB3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_A0A2Y9LH45_A0A2Y9LH45_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_A0A2Y9P805_A0A2Y9P805_DELLE_9749 are exactly identical! WARNING: Sequences tr_H0Y192_H0Y192_OTOGA_30611 and tr_A0A2Y9FFZ4_A0A2Y9FFZ4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G9NQD5_G9NQD5_HYPAI_452589 and tr_A0A2T3YY24_A0A2T3YY24_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_A0A286X9J3_A0A286X9J3_CAVPO_10141 and tr_G5AXI1_G5AXI1_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A1P6C5R6_A0A1P6C5R6_BRUMA_6279 and tr_A0A158PRY0_A0A158PRY0_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_G7XWD5_G7XWD5_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A100IN07_A0A100IN07_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A146FWP0_A0A146FWP0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A1L9NID3_A0A1L9NID3_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A1L9U8R6_A0A1L9U8R6_9EURO_767769 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A317VBL4_A0A317VBL4_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2QGY8_A2QGY8_ASPNC_425011 and tr_A0A319B4Y5_A0A319B4Y5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_G7XJE7_G7XJE7_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_G3XNJ8_G3XNJ8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A100IKQ2_A0A100IKQ2_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A146FHA3_A0A146FHA3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A1L9NKT5_A0A1L9NKT5_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A1L9UZ78_A0A1L9UZ78_9EURO_767769 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A317VU57_A0A317VU57_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A319AQP3_A0A319AQP3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7H7P4_F7H7P4_MACMU_9544 and tr_A0A2K6BXB2_A0A2K6BXB2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H1VPF1_H1VPF1_COLHI_759273 and tr_E3QR15_E3QR15_COLGM_645133 are exactly identical! WARNING: Sequences tr_H1VPF1_H1VPF1_COLHI_759273 and tr_A0A066XK84_A0A066XK84_COLSU_1173701 are exactly identical! WARNING: Sequences tr_H1VPF1_H1VPF1_COLHI_759273 and tr_A0A166SJQ3_A0A166SJQ3_9PEZI_708197 are exactly identical! WARNING: Sequences tr_H1VPF1_H1VPF1_COLHI_759273 and tr_A0A162PF36_A0A162PF36_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_G3NJK0_G3NJK0_GASAC_69293 and tr_A0A2U9AZW4_A0A2U9AZW4_SCOMX_52904 are exactly identical! WARNING: Sequences tr_H0Z3I7_H0Z3I7_TAEGU_59729 and tr_U3JRF7_U3JRF7_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z3I7_H0Z3I7_TAEGU_59729 and tr_A0A218US16_A0A218US16_9PASE_299123 are exactly identical! WARNING: Sequences tr_G2YI01_G2YI01_BOTF4_999810 and tr_M7TP45_M7TP45_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A2R8MNU4_A0A2R8MNU4_CALJA_9483 and tr_A0A0D9QUW5_A0A0D9QUW5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_E3MC61_E3MC61_CAERE_31234 and tr_A0A261CM01_A0A261CM01_9PELO_1503980 are exactly identical! WARNING: Sequences sp_A8WJR8_MBK2_CAEBR_6238 and tr_A0A2G5U663_A0A2G5U663_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3S5V9_B3S5V9_TRIAD_10228 and tr_A0A369RXD8_A0A369RXD8_9METZ_287889 are exactly identical! WARNING: Sequences tr_L2GI48_L2GI48_COLFN_1213859 and tr_T0L599_T0L599_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M2SNF6_M2SNF6_COCSN_665912 and tr_M2SJD1_M2SJD1_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SNF6_M2SNF6_COCSN_665912 and tr_W6Y999_W6Y999_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2SNF6_M2SNF6_COCSN_665912 and tr_W6Z7D9_W6Z7D9_COCMI_930090 are exactly identical! WARNING: Sequences tr_U5H4F3_U5H4F3_USTV1_683840 and tr_A0A2X0P6T1_A0A2X0P6T1_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XCA4_V2XCA4_MONRO_1381753 and tr_A0A0W0G820_A0A0W0G820_9AGAR_221103 are exactly identical! WARNING: Sequences tr_S7ZQ02_S7ZQ02_PENO1_933388 and tr_A0A0F7TK36_A0A0F7TK36_9EURO_104259 are exactly identical! WARNING: Sequences tr_W9WIA9_W9WIA9_9EURO_1182544 and tr_A0A0D2CND3_A0A0D2CND3_9EURO_5601 are exactly identical! WARNING: Sequences tr_W9WIA9_W9WIA9_9EURO_1182544 and tr_A0A1C1CRT2_A0A1C1CRT2_9EURO_86049 are exactly identical! WARNING: Sequences tr_A0A015LPX9_A0A015LPX9_9GLOM_1432141 and tr_A0A2H5TV43_A0A2H5TV43_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A068SBI9_A0A068SBI9_9FUNG_1263082 and tr_A0A068SGN4_A0A068SGN4_9FUNG_1263082 are exactly identical! WARNING: Sequences tr_A0A074WKT7_A0A074WKT7_9PEZI_1043004 and tr_A0A074VYB6_A0A074VYB6_9PEZI_1043003 are exactly identical! WARNING: Sequences tr_A0A091DCD9_A0A091DCD9_FUKDA_885580 and tr_A0A384A8Z7_A0A384A8Z7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A094F6H0_A0A094F6H0_9PEZI_1420910 and tr_A0A094E4V5_A0A094E4V5_9PEZI_1420912 are exactly identical! WARNING: Sequences tr_A0A094F6H0_A0A094F6H0_9PEZI_1420910 and tr_A0A1B8E0J5_A0A1B8E0J5_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094F6H0_A0A094F6H0_9PEZI_1420910 and tr_A0A2P2SVN3_A0A2P2SVN3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094F6H0_A0A094F6H0_9PEZI_1420910 and tr_A0A1B8C396_A0A1B8C396_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094F6H0_A0A094F6H0_9PEZI_1420910 and tr_A0A1B8F330_A0A1B8F330_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A0G4PBZ5_A0A0G4PBZ5_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A135LXV7_A0A135LXV7_PENPA_5078 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A1F5L6M5_A0A1F5L6M5_9EURO_1835702 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A1V6NJ79_A0A1V6NJ79_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A1V6SD87_A0A1V6SD87_9EURO_29845 are exactly identical! WARNING: Sequences tr_A0A0A2KNW8_A0A0A2KNW8_PENIT_40296 and tr_A0A1V6Q015_A0A1V6Q015_9EURO_416450 are exactly identical! WARNING: Sequences tr_A0A0E9NCT1_A0A0E9NCT1_SAICN_698492 and tr_A0A0E9NDM3_A0A0E9NDM3_SAICN_698492 are exactly identical! WARNING: Sequences tr_A0A0F0I044_A0A0F0I044_ASPPU_1403190 and tr_A0A2G7FIM5_A0A2G7FIM5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F0I9F4_A0A0F0I9F4_ASPPU_1403190 and tr_A0A1F8A6M8_A0A1F8A6M8_9EURO_109264 are exactly identical! WARNING: Sequences tr_A0A0F0I9F4_A0A0F0I9F4_ASPPU_1403190 and tr_A0A2G7G4E8_A0A2G7G4E8_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8TZH8_A0A0F8TZH8_9EURO_308745 and tr_A0A2T5LVG1_A0A2T5LVG1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0M9WE28_A0A0M9WE28_9EURO_229535 and tr_A0A0G4P224_A0A0G4P224_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0M9WE28_A0A0M9WE28_9EURO_229535 and tr_A0A117NSD0_A0A117NSD0_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0M9WE28_A0A0M9WE28_9EURO_229535 and tr_A0A1V6QUQ0_A0A1V6QUQ0_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0N0DH06_A0A0N0DH06_FUSLA_179993 and tr_I1RN54_I1RN54_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0N0DH06_A0A0N0DH06_FUSLA_179993 and tr_A0A1B8AKV4_A0A1B8AKV4_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0N0DH06_A0A0N0DH06_FUSLA_179993 and tr_A0A2T4GLL8_A0A2T4GLL8_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0N0DH06_A0A0N0DH06_FUSLA_179993 and tr_A0A2L2TWA3_A0A2L2TWA3_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A0N0DH06_A0A0N0DH06_FUSLA_179993 and tr_A0A366QRC8_A0A366QRC8_9HYPO_2109339 are exactly identical! WARNING: Sequences tr_A0A0D2FEZ4_A0A0D2FEZ4_9EURO_1442368 and tr_A0A178ZKE9_A0A178ZKE9_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A091VWT7_A0A091VWT7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A087R962_A0A087R962_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A091VZ88_A0A091VZ88_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A091G451_A0A091G451_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A0A0AWG3_A0A0A0AWG3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A2I0MSK1_A0A2I0MSK1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A091I493_A0A091I493_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JAZ2_A0A091JAZ2_EGRGA_188379 and tr_A0A1V4J309_A0A1V4J309_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0D2KVT2_A0A0D2KVT2_9EURO_1442371 and tr_A0A0D1ZWK3_A0A0D1ZWK3_9EURO_569365 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V1CQG0_A0A0V1CQG0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V0WDL6_A0A0V0WDL6_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V0VAF7_A0A0V0VAF7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V1L6G6_A0A0V1L6G6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V1A4B3_A0A0V1A4B3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V1NT51_A0A0V1NT51_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RWM5_A0A0V0RWM5_9BILA_6336 and tr_A0A0V0UDW9_A0A0V0UDW9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CYX0_A0A0V1CYX0_TRIBR_45882 and tr_A0A0V1LNJ0_A0A0V1LNJ0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1MGN1_A0A0V1MGN1_9BILA_268474 and tr_A0A0V1GZ81_A0A0V1GZ81_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A194XI92_A0A194XI92_9HELO_149040 and tr_A0A1L7X2H1_A0A1L7X2H1_9HELO_576137 are exactly identical! WARNING: Sequences tr_A0A151WKP4_A0A151WKP4_9HYME_64791 and tr_A0A195ECK3_A0A195ECK3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151WKP4_A0A151WKP4_9HYME_64791 and tr_A0A195EUJ4_A0A195EUJ4_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A164QQ72_A0A164QQ72_9HOMO_1314777 and tr_A0A165Z6S3_A0A165Z6S3_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A194VJA9_A0A194VJA9_9PEZI_105487 and tr_A0A194VB93_A0A194VB93_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A194VJA9_A0A194VJA9_9PEZI_105487 and tr_A0A2P5HG60_A0A2P5HG60_9PEZI_158607 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K8H6_A0A1S3K8H6_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K8H9_A0A1S3K8H9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K908_A0A1S3K908_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3NT95_A0A1S3NT95_SALSA_8030 and tr_A0A060WW27_A0A060WW27_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3T122_A0A1S3T122_SALSA_8030 and tr_A0A060XGB6_A0A060XGB6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A319C6L2_A0A319C6L2_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A319EUR4_A0A319EUR4_9EURO_1448318 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A2V5I4P3_A0A2V5I4P3_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A395I5T6_A0A395I5T6_9EURO_1450537 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A395GNT9_A0A395GNT9_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A1L9WID6_A0A1L9WID6_ASPAC_690307 and tr_A0A2V5HIX2_A0A2V5HIX2_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A1D1W0F8_A0A1D1W0F8_RAMVA_947166 and tr_A0A1D1W2W7_A0A1D1W2W7_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1R3RA30_A0A1R3RA30_ASPC5_602072 and tr_A0A317V3Q8_A0A317V3Q8_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A2N5T2P5_A0A2N5T2P5_9BASI_200324 and tr_A0A2N5W1Q9_A0A2N5W1Q9_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2J6PLA3_A0A2J6PLA3_9HELO_1745343 and tr_A0A2J6RYR6_A0A2J6RYR6_9HELO_1149755 are exactly identical! WARNING: Sequences tr_A0A2T4C1J6_A0A2T4C1J6_TRILO_983965 and tr_A0A2T4AYU5_A0A2T4AYU5_9HYPO_58853 are exactly identical! WARNING: Sequences tr_A0A2V5I405_A0A2V5I405_9EURO_1450541 and tr_A0A2V5HE43_A0A2V5HE43_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 200 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/Q13627/3_mltree/Q13627.raxml.reduced.phy Alignment comprises 1 partitions and 349 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 350 / 349 Gaps: 1.83 % Invariant sites: 3.71 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 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 / 349 / 27920 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -512857.183780] Initial branch length optimization [00:00:09 -419604.089120] Model parameter optimization (eps = 10.000000) [00:01:19 -418606.528066] AUTODETECT spr round 1 (radius: 5) [00:05:49 -246890.272730] AUTODETECT spr round 2 (radius: 10) [00:10:18 -183520.094221] AUTODETECT spr round 3 (radius: 15) [00:14:46 -146941.421216] AUTODETECT spr round 4 (radius: 20) [00:20:04 -125084.158141] AUTODETECT spr round 5 (radius: 25) [00:26:10 -118515.288121] SPR radius for FAST iterations: 25 (autodetect) [00:26:10 -118515.288121] Model parameter optimization (eps = 3.000000) [00:26:38 -118459.117330] FAST spr round 1 (radius: 25) [00:31:08 -97597.764965] FAST spr round 2 (radius: 25) [00:34:12 -96705.313930] FAST spr round 3 (radius: 25) [00:37:04 -96643.520686] FAST spr round 4 (radius: 25) [00:39:44 -96627.897658] FAST spr round 5 (radius: 25) [00:42:15 -96622.402311] FAST spr round 6 (radius: 25) [00:44:39 -96611.500606] FAST spr round 7 (radius: 25) [00:46:58 -96611.499988] Model parameter optimization (eps = 1.000000) [00:47:12 -96609.972169] SLOW spr round 1 (radius: 5) [00:50:27 -96584.780864] SLOW spr round 2 (radius: 5) [00:53:38 -96580.404214] SLOW spr round 3 (radius: 5) [00:56:46 -96578.253808] SLOW spr round 4 (radius: 5) [00:59:41 -96577.439882] SLOW spr round 5 (radius: 5) [01:02:27 -96577.439613] SLOW spr round 6 (radius: 10) [01:05:34 -96574.622781] SLOW spr round 7 (radius: 5) [01:09:22 -96573.762788] SLOW spr round 8 (radius: 5) [01:12:55 -96572.783225] SLOW spr round 9 (radius: 5) [01:16:07 -96572.783080] SLOW spr round 10 (radius: 10) [01:19:06] [worker #4] ML tree search #5, logLikelihood: -96571.167112 [01:19:31 -96572.783014] SLOW spr round 11 (radius: 15) [01:24:36 -96572.782953] SLOW spr round 12 (radius: 20) [01:31:19] [worker #1] ML tree search #2, logLikelihood: -96548.982722 [01:31:59 -96571.691451] SLOW spr round 13 (radius: 5) [01:36:13] [worker #3] ML tree search #4, logLikelihood: -96558.689599 [01:36:27 -96571.691429] SLOW spr round 14 (radius: 10) [01:40:32 -96571.691410] SLOW spr round 15 (radius: 15) [01:44:28] [worker #2] ML tree search #3, logLikelihood: -96569.557912 [01:45:31 -96571.691392] SLOW spr round 16 (radius: 20) [01:53:04 -96571.691375] SLOW spr round 17 (radius: 25) [02:02:26 -96571.691360] Model parameter optimization (eps = 0.100000) [02:02:41] [worker #0] ML tree search #1, logLikelihood: -96571.526245 [02:02:41 -516559.352158] Initial branch length optimization [02:02:51 -426038.358402] Model parameter optimization (eps = 10.000000) [02:03:52 -425137.868082] AUTODETECT spr round 1 (radius: 5) [02:08:20 -249971.033038] AUTODETECT spr round 2 (radius: 10) [02:12:48 -190359.339943] AUTODETECT spr round 3 (radius: 15) [02:17:31 -151070.457384] AUTODETECT spr round 4 (radius: 20) [02:22:46 -133267.090210] AUTODETECT spr round 5 (radius: 25) [02:28:11 -124485.401208] SPR radius for FAST iterations: 25 (autodetect) [02:28:11 -124485.401208] Model parameter optimization (eps = 3.000000) [02:28:44 -124415.335666] FAST spr round 1 (radius: 25) [02:33:00 -100283.094392] FAST spr round 2 (radius: 25) [02:36:08 -97397.603676] FAST spr round 3 (radius: 25) [02:38:59 -96684.235236] FAST spr round 4 (radius: 25) [02:41:35 -96602.807911] FAST spr round 5 (radius: 25) [02:44:04 -96596.283769] FAST spr round 6 (radius: 25) [02:46:21 -96596.283548] Model parameter optimization (eps = 1.000000) [02:46:41 -96587.381388] SLOW spr round 1 (radius: 5) [02:49:55 -96575.229135] SLOW spr round 2 (radius: 5) [02:53:02 -96570.730163] SLOW spr round 3 (radius: 5) [02:56:03 -96570.729754] SLOW spr round 4 (radius: 10) [02:59:24 -96570.729746] SLOW spr round 5 (radius: 15) [03:01:05] [worker #1] ML tree search #7, logLikelihood: -96567.315364 [03:04:37 -96570.729741] SLOW spr round 6 (radius: 20) [03:12:26] [worker #2] ML tree search #8, logLikelihood: -96585.463386 [03:12:30 -96570.729737] SLOW spr round 7 (radius: 25) [03:15:54] [worker #4] ML tree search #10, logLikelihood: -96568.644405 [03:21:30 -96570.729733] Model parameter optimization (eps = 0.100000) [03:21:34] [worker #0] ML tree search #6, logLikelihood: -96570.728789 [03:21:34 -512764.282926] Initial branch length optimization [03:21:46 -423328.936697] Model parameter optimization (eps = 10.000000) [03:22:46 -422476.518312] AUTODETECT spr round 1 (radius: 5) [03:27:19 -242223.737269] AUTODETECT spr round 2 (radius: 10) [03:31:51 -179413.902695] AUTODETECT spr round 3 (radius: 15) [03:36:35 -145697.562636] AUTODETECT spr round 4 (radius: 20) [03:41:41 -123696.375814] AUTODETECT spr round 5 (radius: 25) [03:42:25] [worker #3] ML tree search #9, logLikelihood: -96565.939457 [03:47:40 -119885.772595] SPR radius for FAST iterations: 25 (autodetect) [03:47:40 -119885.772595] Model parameter optimization (eps = 3.000000) [03:48:07 -119830.086747] FAST spr round 1 (radius: 25) [03:52:37 -98038.702471] FAST spr round 2 (radius: 25) [03:55:39 -96717.945485] FAST spr round 3 (radius: 25) [03:58:18 -96670.772305] FAST spr round 4 (radius: 25) [04:00:51 -96651.090771] FAST spr round 5 (radius: 25) [04:03:18 -96644.377420] FAST spr round 6 (radius: 25) [04:05:35 -96644.377248] Model parameter optimization (eps = 1.000000) [04:05:48 -96643.214124] SLOW spr round 1 (radius: 5) [04:09:01 -96615.742611] SLOW spr round 2 (radius: 5) [04:12:12 -96614.236783] SLOW spr round 3 (radius: 5) [04:15:13 -96614.236770] SLOW spr round 4 (radius: 10) [04:18:36 -96609.302117] SLOW spr round 5 (radius: 5) [04:22:54 -96603.012998] SLOW spr round 6 (radius: 5) [04:26:27 -96602.944783] SLOW spr round 7 (radius: 10) [04:28:40] [worker #1] ML tree search #12, logLikelihood: -96579.545923 [04:29:57 -96598.769586] SLOW spr round 8 (radius: 5) [04:33:59 -96597.660518] SLOW spr round 9 (radius: 5) [04:37:29 -96597.660475] SLOW spr round 10 (radius: 10) [04:37:45] [worker #2] ML tree search #13, logLikelihood: -96563.509095 [04:40:57 -96597.660474] SLOW spr round 11 (radius: 15) [04:46:11 -96597.660474] SLOW spr round 12 (radius: 20) [04:47:13] [worker #4] ML tree search #15, logLikelihood: -96568.726313 [04:54:03 -96558.479878] SLOW spr round 13 (radius: 5) [04:58:34 -96550.089313] SLOW spr round 14 (radius: 5) [05:02:20 -96550.089313] SLOW spr round 15 (radius: 10) [05:05:54 -96550.089312] SLOW spr round 16 (radius: 15) [05:11:07 -96550.089312] SLOW spr round 17 (radius: 20) [05:19:02 -96550.089311] SLOW spr round 18 (radius: 25) [05:21:59] [worker #3] ML tree search #14, logLikelihood: -96601.065453 [05:28:08 -96550.089311] Model parameter optimization (eps = 0.100000) [05:28:16] [worker #0] ML tree search #11, logLikelihood: -96550.070424 [05:28:16 -518899.854454] Initial branch length optimization [05:28:25 -425529.405156] Model parameter optimization (eps = 10.000000) [05:29:21 -424583.266886] AUTODETECT spr round 1 (radius: 5) [05:33:44 -243779.712984] AUTODETECT spr round 2 (radius: 10) [05:38:08 -181817.488132] AUTODETECT spr round 3 (radius: 15) [05:42:39 -153690.749876] AUTODETECT spr round 4 (radius: 20) [05:47:41 -138560.398685] AUTODETECT spr round 5 (radius: 25) [05:49:26] [worker #1] ML tree search #17, logLikelihood: -96551.977205 [05:53:29 -132673.658915] SPR radius for FAST iterations: 25 (autodetect) [05:53:29 -132673.658915] Model parameter optimization (eps = 3.000000) [05:53:59 -132565.068960] FAST spr round 1 (radius: 25) [05:58:39 -101840.330094] FAST spr round 2 (radius: 25) [06:02:17 -97199.846408] FAST spr round 3 (radius: 25) [06:05:22 -96693.581333] FAST spr round 4 (radius: 25) [06:07:58 -96643.346537] FAST spr round 5 (radius: 25) [06:10:18 -96631.650613] FAST spr round 6 (radius: 25) [06:12:34 -96631.649990] Model parameter optimization (eps = 1.000000) [06:12:44] [worker #4] ML tree search #20, logLikelihood: -96565.330792 [06:12:56 -96626.232661] SLOW spr round 1 (radius: 5) [06:16:02 -96594.686186] SLOW spr round 2 (radius: 5) [06:17:16] [worker #2] ML tree search #18, logLikelihood: -96574.851908 [06:19:04 -96594.051560] SLOW spr round 3 (radius: 5) [06:22:00 -96594.051123] SLOW spr round 4 (radius: 10) [06:25:21 -96589.635682] SLOW spr round 5 (radius: 5) [06:29:21 -96588.396863] SLOW spr round 6 (radius: 5) [06:32:48 -96588.395772] SLOW spr round 7 (radius: 10) [06:36:17 -96584.234671] SLOW spr round 8 (radius: 5) [06:40:14 -96583.174287] SLOW spr round 9 (radius: 5) [06:43:07] [worker #3] ML tree search #19, logLikelihood: -96570.478761 [06:43:41 -96582.517135] SLOW spr round 10 (radius: 5) [06:46:52 -96581.771851] SLOW spr round 11 (radius: 5) [06:49:55 -96579.160423] SLOW spr round 12 (radius: 5) [06:52:54 -96577.899462] SLOW spr round 13 (radius: 5) [06:55:52 -96576.276299] SLOW spr round 14 (radius: 5) [06:58:49 -96575.284841] SLOW spr round 15 (radius: 5) [07:01:44 -96575.284560] SLOW spr round 16 (radius: 10) [07:05:01 -96575.284557] SLOW spr round 17 (radius: 15) [07:10:09 -96575.284556] SLOW spr round 18 (radius: 20) [07:17:54 -96575.284555] SLOW spr round 19 (radius: 25) [07:27:24 -96575.284553] Model parameter optimization (eps = 0.100000) [07:27:31] [worker #0] ML tree search #16, logLikelihood: -96575.244041 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.233469,0.268706) (0.280076,0.449264) (0.311318,1.146376) (0.175137,2.595401) 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: -96548.982722 AIC score: 197107.965445 / AICc score: 8241167.965445 / BIC score: 204843.121419 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=350). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 268 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.log Analysis started: 06-Jul-2021 02:57:34 / finished: 06-Jul-2021 10:25:06 Elapsed time: 26851.749 seconds Consumed energy: 2401.350 Wh (= 12 km in an electric car, or 60 km with an e-scooter!)