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 30-Jun-2021 22:44:43 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/2_msa/O75838_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/2_msa/O75838_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 164 sites WARNING: Sequences tr_B4QFI4_B4QFI4_DROSI_7240 and tr_B4I7F9_B4I7F9_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_Q6VN51_Q6VN51_CHICK_9031 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and sp_Q63810_CANB1_MOUSE_10090 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_H2LAJ9_H2LAJ9_ORYLA_8090 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and sp_P63100_CANB1_RAT_10116 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A3B5QS63_A0A3B5QS63_XIPMA_8083 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A3B5KQF4_A0A3B5KQF4_TAKRU_31033 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and sp_P63098_CANB1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_H3CWS9_H3CWS9_TETNG_99883 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_Q6VN50_Q6VN50_XENTR_8364 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A287ACI6_A0A287ACI6_PIG_9823 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and sp_P63099_CANB1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_U3KGU1_U3KGU1_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A3B1JIC8_A0A3B1JIC8_ASTMX_7994 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A0D9RQT1_A0A0D9RQT1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A151MH36_A0A151MH36_ALLMI_8496 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A0Q3U4K3_A0A0Q3U4K3_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A1L8G736_A0A1L8G736_XENLA_8355 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2I4CLA3_A0A2I4CLA3_9TELE_52670 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A218UVB1_A0A218UVB1_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_W5UB88_W5UB88_ICTPU_7998 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2U3VR26_A0A2U3VR26_ODORO_9708 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2U3XF20_A0A2U3XF20_LEPWE_9713 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2Y9RBM0_A0A2Y9RBM0_TRIMA_127582 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2Y9JQG7_A0A2Y9JQG7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2Y9QC60_A0A2Y9QC60_DELLE_9749 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A2Y9TJR4_A0A2Y9TJR4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_Q66HZ0_Q66HZ0_DANRE_7955 and tr_A0A384CTL9_A0A384CTL9_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Y4E6_M3Y4E6_MUSPF_9669 and tr_F6XK91_F6XK91_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Y4E6_M3Y4E6_MUSPF_9669 and tr_W5QF78_W5QF78_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y4E6_M3Y4E6_MUSPF_9669 and tr_A0A2I0M979_A0A2I0M979_COLLI_8932 are exactly identical! WARNING: Sequences tr_M3Y4E6_M3Y4E6_MUSPF_9669 and tr_A0A1S3FPP0_A0A1S3FPP0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3Y4E6_M3Y4E6_MUSPF_9669 and tr_A0A3Q0DNN3_A0A3Q0DNN3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_Q9W2Q5_Q9W2Q5_DROME_7227 and tr_B3MIR0_B3MIR0_DROAN_7217 are exactly identical! WARNING: Sequences tr_Q9W2Q5_Q9W2Q5_DROME_7227 and tr_A0A1W4VI87_A0A1W4VI87_DROFC_30025 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_B2WKK1_B2WKK1_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_E4ZS47_E4ZS47_LEPMJ_985895 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_M2RTZ9_M2RTZ9_COCSN_665912 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_R0IJS1_R0IJS1_SETT2_671987 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_M2U850_M2U850_COCH5_701091 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_W6ZPW0_W6ZPW0_COCMI_930090 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_A0A177DWN2_A0A177DWN2_ALTAL_5599 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_A0A2W1GEM5_A0A2W1GEM5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_E3S6J0_E3S6J0_PYRTT_861557 and tr_A0A364N4P7_A0A364N4P7_9PLEO_183478 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2I2YXV6_A0A2I2YXV6_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_F7HKB4_F7HKB4_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2R8PIG5_A0A2R8PIG5_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2I3LGY3_A0A2I3LGY3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2K5MJM5_A0A2K5MJM5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2K6E099_A0A2K6E099_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3G398_A0A2I3G398_NOMLE_61853 and tr_A0A2K5ZJX2_A0A2K5ZJX2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_G3R5U3_G3R5U3_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_H2Q9V9_H2Q9V9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and sp_O75838_CIB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_A0A1D5QJW5_A0A1D5QJW5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_A0A0D9RQJ0_A0A0D9RQJ0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_A0A2K5LDZ0_A0A2K5LDZ0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HXJ9_A0A2I3HXJ9_NOMLE_61853 and tr_A0A2R9C2G8_A0A2R9C2G8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PGU3_G1PGU3_MYOLU_59463 and tr_A0A2U3V0K4_A0A2U3V0K4_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3H0B4_G3H0B4_CRIGR_10029 and sp_Q568Z7_CIB2_RAT_10116 are exactly identical! WARNING: Sequences tr_G3H0B4_G3H0B4_CRIGR_10029 and tr_I3NBB3_I3NBB3_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3H0B4_G3H0B4_CRIGR_10029 and tr_A0A091DXW3_A0A091DXW3_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G3H0B4_G3H0B4_CRIGR_10029 and tr_A0A1U7QAI0_A0A1U7QAI0_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2Z4F1_A0A2I2Z4F1_GORGO_9595 and sp_Q99828_CIB1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R579_G3R579_GORGO_9595 and tr_H2QHK6_H2QHK6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R579_G3R579_GORGO_9595 and tr_A0A0D9RA58_A0A0D9RA58_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R579_G3R579_GORGO_9595 and tr_A0A2K5M8F7_A0A2K5M8F7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R579_G3R579_GORGO_9595 and tr_A0A2K6CV04_A0A2K6CV04_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R579_G3R579_GORGO_9595 and tr_A0A2K5XZ19_A0A2K5XZ19_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1MXR6_G1MXR6_MELGA_9103 and tr_H0YYG7_H0YYG7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1MXR6_G1MXR6_MELGA_9103 and tr_U3I405_U3I405_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1MXR6_G1MXR6_MELGA_9103 and tr_A0A1V4JDF6_A0A1V4JDF6_PATFA_372326 are exactly identical! WARNING: Sequences tr_B8PDB7_B8PDB7_POSPM_561896 and tr_A0A1X6MVY8_A0A1X6MVY8_9APHY_670580 are exactly identical! WARNING: Sequences sp_P87072_CANB_NEUCR_367110 and tr_G4UDQ2_G4UDQ2_NEUT9_510952 are exactly identical! WARNING: Sequences sp_G5EDN6_CANB_CAEEL_6239 and tr_G0P6N0_G0P6N0_CAEBE_135651 are exactly identical! WARNING: Sequences sp_G5EDN6_CANB_CAEEL_6239 and tr_A8Y4I1_A8Y4I1_CAEBR_6238 are exactly identical! WARNING: Sequences sp_G5EDN6_CANB_CAEEL_6239 and tr_A0A1I7TX32_A0A1I7TX32_9PELO_1561998 are exactly identical! WARNING: Sequences sp_G5EDN6_CANB_CAEEL_6239 and tr_A0A2G5TI26_A0A2G5TI26_9PELO_1611254 are exactly identical! WARNING: Sequences tr_Q93640_Q93640_CAEEL_6239 and tr_G0MEY9_G0MEY9_CAEBE_135651 are exactly identical! WARNING: Sequences tr_Q93640_Q93640_CAEEL_6239 and tr_A0A1I7U4U5_A0A1I7U4U5_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A179UX20_A0A179UX20_BLAGS_559298 and tr_C5GLM4_C5GLM4_AJEDR_559297 are exactly identical! WARNING: Sequences tr_J9P800_J9P800_CANLF_9615 and tr_F6SEN5_F6SEN5_HORSE_9796 are exactly identical! WARNING: Sequences tr_H2QFP0_H2QFP0_PANTR_9598 and tr_A0A2R9C7H3_A0A2R9C7H3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7C6H2_F7C6H2_MONDO_13616 and tr_H1A4T1_H1A4T1_TAEGU_59729 are exactly identical! WARNING: Sequences tr_F7C6H2_F7C6H2_MONDO_13616 and tr_A0A093SRM3_A0A093SRM3_9PASS_328815 are exactly identical! WARNING: Sequences tr_F7C6H2_F7C6H2_MONDO_13616 and tr_A0A099Z538_A0A099Z538_TINGU_94827 are exactly identical! WARNING: Sequences sp_B1A8Z2_CIB1_SHEEP_9940 and sp_Q17QE5_CIB1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_C7A278_CIB4_SHEEP_9940 and tr_W5QCB8_W5QCB8_SHEEP_9940 are exactly identical! WARNING: Sequences sp_C7A278_CIB4_SHEEP_9940 and tr_F1MQC6_F1MQC6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FLH3_F9FLH3_FUSOF_660025 and tr_A0A0D2XC66_A0A0D2XC66_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FLH3_F9FLH3_FUSOF_660025 and tr_X0D078_X0D078_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FLH3_F9FLH3_FUSOF_660025 and tr_A0A1B8ADV6_A0A1B8ADV6_FUSPO_36050 are exactly identical! WARNING: Sequences tr_F9FLH3_F9FLH3_FUSOF_660025 and tr_A0A2H3T5J9_A0A2H3T5J9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FLH3_F9FLH3_FUSOF_660025 and tr_A0A2H3HBS5_A0A2H3HBS5_FUSOX_327505 are exactly identical! WARNING: Sequences sp_Q9R010_CIB1_RAT_10116 and tr_A0A1U7R205_A0A1U7R205_MESAU_10036 are exactly identical! WARNING: Sequences tr_E9F4Z5_E9F4Z5_METRA_655844 and tr_A0A0D9NZ87_A0A0D9NZ87_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9F4Z5_E9F4Z5_METRA_655844 and tr_A0A167KPJ0_A0A167KPJ0_9HYPO_1081105 are exactly identical! WARNING: Sequences tr_C6HHU8_C6HHU8_AJECH_544712 and tr_F0UR73_F0UR73_AJEC8_544711 are exactly identical! WARNING: Sequences tr_C7YTK9_C7YTK9_NECH7_660122 and tr_A0A2L2TGT6_A0A2L2TGT6_9HYPO_56646 are exactly identical! WARNING: Sequences tr_I3MS58_I3MS58_ICTTR_43179 and tr_A0A286Y2C2_A0A286Y2C2_CAVPO_10141 are exactly identical! WARNING: Sequences tr_I3MS58_I3MS58_ICTTR_43179 and tr_G3TMG5_G3TMG5_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A3B5KKN7_A0A3B5KKN7_TAKRU_31033 and tr_G3Q7X8_G3Q7X8_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A0C4EN69_A0A0C4EN69_PUCT1_630390 and tr_A0A0L0VCL4_A0A0L0VCL4_9BASI_1165861 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_G9MEC8_G9MEC8_HYPVG_413071 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_G0RV16_G0RV16_HYPJQ_431241 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_A0A2P5A141_A0A2P5A141_9HYPO_398673 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_A0A2T3YS91_A0A2T3YS91_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_A0A2T4CE08_A0A2T4CE08_TRILO_983965 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_A0A2T4B0H7_A0A2T4B0H7_9HYPO_58853 are exactly identical! WARNING: Sequences tr_G9NF52_G9NF52_HYPAI_452589 and tr_A0A2T4A6G1_A0A2T4A6G1_TRIHA_983964 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_H1VQE3_H1VQE3_COLHI_759273 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_N4V911_N4V911_COLOR_1213857 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A010QEM9_A0A010QEM9_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A135RMK2_A0A135RMK2_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A167EGK6_A0A167EGK6_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A179H761_A0A179H761_9HYPO_33203 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A1G4AVP4_A0A1G4AVP4_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_J3NY07_J3NY07_GAGT3_644352 and tr_A0A1Y2X797_A0A1Y2X797_9PEZI_1001832 are exactly identical! WARNING: Sequences tr_A0A0J9Y6X5_A0A0J9Y6X5_BRUMA_6279 and tr_A0A0N4T2M8_A0A0N4T2M8_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0J9Y6X5_A0A0J9Y6X5_BRUMA_6279 and tr_A0A0R3R6Y3_A0A0R3R6Y3_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A0J9Y6X5_A0A0J9Y6X5_BRUMA_6279 and tr_A0A0R3S696_A0A0R3S696_9BILA_1147741 are exactly identical! WARNING: Sequences tr_A0A0J9Y6X5_A0A0J9Y6X5_BRUMA_6279 and tr_A0A1I7W5K3_A0A1I7W5K3_LOALO_7209 are exactly identical! WARNING: Sequences tr_A0A0K0JEL2_A0A0K0JEL2_BRUMA_6279 and tr_A0A0N4TYC6_A0A0N4TYC6_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F6ZM15_F6ZM15_MACMU_9544 and tr_G7PZQ1_G7PZQ1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZM15_F6ZM15_MACMU_9544 and tr_A0A2K5LCL6_A0A2K5LCL6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZM15_F6ZM15_MACMU_9544 and tr_A0A2K6EBE5_A0A2K6EBE5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MVY1_G7MVY1_MACMU_9544 and tr_A0A096NN98_A0A096NN98_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MVY1_G7MVY1_MACMU_9544 and tr_A0A0D9RX03_A0A0D9RX03_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G5BA16_G5BA16_HETGA_10181 and tr_A0A093I8L9_A0A093I8L9_STRCA_441894 are exactly identical! WARNING: Sequences tr_G5BA16_G5BA16_HETGA_10181 and tr_A0A0A0AHC7_A0A0A0AHC7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_E5S206_E5S206_TRISP_6334 and tr_A0A0V0U342_A0A0V0U342_9BILA_144512 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0RK17_A0A0V0RK17_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V1CKD7_A0A0V1CKD7_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0W846_A0A0V0W846_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0UL74_A0A0V0UL74_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V1LF53_A0A0V1LF53_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0Z703_A0A0V0Z703_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0XYS6_A0A0V0XYS6_TRIPS_6337 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V1M7G5_A0A0V1M7G5_9BILA_268474 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V1NIL6_A0A0V1NIL6_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V1HTN8_A0A0V1HTN8_9BILA_268475 are exactly identical! WARNING: Sequences tr_E5SLN1_E5SLN1_TRISP_6334 and tr_A0A0V0T8I6_A0A0V0T8I6_9BILA_144512 are exactly identical! WARNING: Sequences tr_F4X5F4_F4X5F4_ACREC_103372 and tr_A0A195DPF2_A0A195DPF2_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4X5F4_F4X5F4_ACREC_103372 and tr_A0A195BNE3_A0A195BNE3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F4X5F4_F4X5F4_ACREC_103372 and tr_A0A195EZ36_A0A195EZ36_9HYME_34720 are exactly identical! WARNING: Sequences tr_F4X5F4_F4X5F4_ACREC_103372 and tr_A0A195CEE0_A0A195CEE0_9HYME_456900 are exactly identical! WARNING: Sequences tr_F9X3U4_F9X3U4_ZYMTI_336722 and tr_A0A0F4GSU1_A0A0F4GSU1_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9X3U4_F9X3U4_ZYMTI_336722 and tr_A0A1X7RKF0_A0A1X7RKF0_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_E3MQD1_E3MQD1_CAERE_31234 and tr_A0A261BDX3_A0A261BDX3_9PELO_1503980 are exactly identical! WARNING: Sequences tr_C9S8J4_C9S8J4_VERA1_526221 and tr_A0A0G4MNL1_A0A0G4MNL1_9PEZI_100787 are exactly identical! WARNING: Sequences tr_E3QB66_E3QB66_COLGM_645133 and tr_A0A066X9T2_A0A066X9T2_COLSU_1173701 are exactly identical! WARNING: Sequences tr_E3K1Y3_E3K1Y3_PUCGT_418459 and tr_A0A2N5VVQ8_A0A2N5VVQ8_9BASI_200324 are exactly identical! WARNING: Sequences tr_G1LTJ3_G1LTJ3_AILME_9646 and tr_A0A2U3W8M6_A0A2U3W8M6_ODORO_9708 are exactly identical! WARNING: Sequences tr_B3S1A7_B3S1A7_TRIAD_10228 and tr_A0A369S953_A0A369S953_9METZ_287889 are exactly identical! WARNING: Sequences tr_R9PFV4_R9PFV4_PSEHS_1305764 and tr_A0A0F7S340_A0A0F7S340_9BASI_49012 are exactly identical! WARNING: Sequences tr_S0DW13_S0DW13_GIBF5_1279085 and tr_A0A365MQD4_A0A365MQD4_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2XL22_V2XL22_MONRO_1381753 and tr_A0A0W0GDX6_A0A0W0GDX6_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015JVW1_A0A015JVW1_9GLOM_1432141 and tr_A0A2I1DSV8_A0A2I1DSV8_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A2K6VRN0_A0A2K6VRN0_ONCVO_6282 and tr_A0A182EH45_A0A182EH45_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NMV2_A0A096NMV2_PAPAN_9555 and tr_A0A2K6C1L7_A0A2K6C1L7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A2VI07_A0A0A2VI07_BEABA_1245745 and tr_A0A168CNH7_A0A168CNH7_9HYPO_1081104 are exactly identical! WARNING: Sequences tr_A0A0A2VI07_A0A0A2VI07_BEABA_1245745 and tr_A0A167FID4_A0A167FID4_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_A0A0A2VI07_A0A0A2VI07_BEABA_1245745 and tr_A0A168H6W3_A0A168H6W3_CORDF_1081108 are exactly identical! WARNING: Sequences tr_A0A0A2VI07_A0A0A2VI07_BEABA_1245745 and tr_A0A2N6NKU7_A0A2N6NKU7_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0K0F9D4_A0A0K0F9D4_STRVS_75913 and tr_A0A0N5C8N8_A0A0N5C8N8_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0K0EQL5_A0A0K0EQL5_STRER_6248 and tr_A0A0N5CDJ1_A0A0N5CDJ1_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0M9F4L4_A0A0M9F4L4_FUSLA_179993 and tr_I1RTA3_I1RTA3_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0M9F4L4_A0A0M9F4L4_FUSLA_179993 and tr_A0A2T4H4B9_A0A2T4H4B9_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0A1NIQ3_A0A0A1NIQ3_9FUNG_58291 and tr_A0A2G4SJQ6_A0A2G4SJQ6_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1NIQ3_A0A0A1NIQ3_9FUNG_58291 and tr_A0A367KD21_A0A367KD21_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0R3WJC4_A0A0R3WJC4_HYDTA_6205 and tr_A0A0R3VUQ2_A0A0R3VUQ2_TAEAS_60517 are exactly identical! WARNING: Sequences tr_A0A091F9B8_A0A091F9B8_CORBR_85066 and tr_A0A099ZKP5_A0A099ZKP5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A091VQR9_A0A091VQR9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A087QH66_A0A087QH66_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A091WF88_A0A091WF88_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A091GFP3_A0A091GFP3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A093GMD4_A0A093GMD4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091K4Q2_A0A091K4Q2_EGRGA_188379 and tr_A0A091HZQ5_A0A091HZQ5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091VHZ3_A0A091VHZ3_NIPNI_128390 and tr_A0A093I0K0_A0A093I0K0_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091VHZ3_A0A091VHZ3_NIPNI_128390 and tr_A0A091WPJ1_A0A091WPJ1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091VHZ3_A0A091VHZ3_NIPNI_128390 and tr_A0A0A0AJJ8_A0A0A0AJJ8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_W6YQF0_W6YQF0_COCCA_930089 and tr_A0A178DLL1_A0A178DLL1_9PLEO_765867 are exactly identical! WARNING: Sequences tr_A0A0C9ZE31_A0A0C9ZE31_9HOMO_765257 and tr_A0A0C3P6U3_A0A0C3P6U3_PISTI_870435 are exactly identical! WARNING: Sequences tr_A0A0D0B8Z7_A0A0D0B8Z7_9HOMO_930992 and tr_A0A1B7N324_A0A1B7N324_9HOMO_1314800 are exactly identical! WARNING: Sequences tr_A0A0D0B8Z7_A0A0D0B8Z7_9HOMO_930992 and tr_A0A1J8QBA2_A0A1J8QBA2_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A0P1B8Z8_A0A0P1B8Z8_9BASI_401625 and tr_A0A316VVN9_A0A316VVN9_9BASI_1522189 are exactly identical! WARNING: Sequences tr_A0A164ZPE8_A0A164ZPE8_9HOMO_1314777 and tr_A0A166HSD3_A0A166HSD3_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A194W3L9_A0A194W3L9_9PEZI_105487 and tr_A0A194V1S1_A0A194V1S1_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1A6ACC0_A0A1A6ACC0_9TREE_1296121 and tr_A0A1B9HVV8_A0A1B9HVV8_9TREE_1296096 are exactly identical! WARNING: Sequences tr_A0A1V8UEG1_A0A1V8UEG1_9PEZI_1974281 and tr_A0A1V8T3K0_A0A1V8T3K0_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y2V744_A0A1Y2V744_9PEZI_1001938 and tr_A0A1Y2W7J6_A0A1Y2W7J6_9PEZI_1001833 are exactly identical! WARNING: Sequences tr_A0A2K5NB57_A0A2K5NB57_CERAT_9531 and tr_A0A2K6AZN9_A0A2K6AZN9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K3QIN8_A0A2K3QIN8_9HYPO_45235 and tr_A0A2S4KT09_A0A2S4KT09_9HYPO_94208 are exactly identical! WARNING: Sequences tr_A0A2S7PQN3_A0A2S7PQN3_9HELO_2070414 and tr_A0A2S7QW15_A0A2S7QW15_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2Y9MKZ4_A0A2Y9MKZ4_DELLE_9749 and tr_A0A2Y9ENQ0_A0A2Y9ENQ0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9EKR9_A0A2Y9EKR9_PHYCD_9755 and tr_A0A383ZF73_A0A383ZF73_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2X0M9W7_A0A2X0M9W7_9BASI_796604 and tr_A0A2X0NJP2_A0A2X0NJP2_9BASI_289078 are exactly identical! WARNING: Sequences tr_A0A369GKW6_A0A369GKW6_9HYPO_2039875 and tr_A0A367KZ40_A0A367KZ40_9HYPO_1330021 are exactly identical! WARNING: Duplicate sequences found: 198 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/O75838/3_mltree/O75838.raxml.reduced.phy Alignment comprises 1 partitions and 164 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 164 / 164 Gaps: 3.73 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.rba Parallelization scheme autoconfig: 3 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 / 164 / 13120 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -275969.255533] Initial branch length optimization [00:00:05 -220726.802465] Model parameter optimization (eps = 10.000000) [00:00:41 -220229.878825] AUTODETECT spr round 1 (radius: 5) [00:03:13 -136367.842647] AUTODETECT spr round 2 (radius: 10) [00:05:45 -99142.451266] AUTODETECT spr round 3 (radius: 15) [00:08:23 -79011.480354] AUTODETECT spr round 4 (radius: 20) [00:11:13 -70096.010538] AUTODETECT spr round 5 (radius: 25) [00:14:30 -65961.160169] SPR radius for FAST iterations: 25 (autodetect) [00:14:30 -65961.160169] Model parameter optimization (eps = 3.000000) [00:14:53 -65921.526601] FAST spr round 1 (radius: 25) [00:17:43 -53207.838356] FAST spr round 2 (radius: 25) [00:19:49 -50479.925903] FAST spr round 3 (radius: 25) [00:21:44 -50022.045220] FAST spr round 4 (radius: 25) [00:23:36 -49962.341842] FAST spr round 5 (radius: 25) [00:25:19 -49961.732313] FAST spr round 6 (radius: 25) [00:26:57 -49961.732239] Model parameter optimization (eps = 1.000000) [00:27:23 -49918.901199] SLOW spr round 1 (radius: 5) [00:29:29 -49899.782259] SLOW spr round 2 (radius: 5) [00:31:35 -49892.790582] SLOW spr round 3 (radius: 5) [00:33:39 -49892.461403] SLOW spr round 4 (radius: 5) [00:35:41 -49892.461349] SLOW spr round 5 (radius: 10) [00:37:50 -49889.477846] SLOW spr round 6 (radius: 5) [00:40:20 -49889.477400] SLOW spr round 7 (radius: 10) [00:42:39 -49880.684109] SLOW spr round 8 (radius: 5) [00:45:11 -49879.200594] SLOW spr round 9 (radius: 5) [00:47:24 -49879.200415] SLOW spr round 10 (radius: 10) [00:49:33 -49876.848068] SLOW spr round 11 (radius: 5) [00:52:02 -49876.848054] SLOW spr round 12 (radius: 10) [00:54:18 -49876.848054] SLOW spr round 13 (radius: 15) [00:57:07 -49876.848054] SLOW spr round 14 (radius: 20) [00:58:04] [worker #1] ML tree search #2, logLikelihood: -49893.192816 [01:01:06 -49876.848054] SLOW spr round 15 (radius: 25) [01:06:10 -49876.253707] SLOW spr round 16 (radius: 5) [01:08:52 -49876.253696] SLOW spr round 17 (radius: 10) [01:11:20 -49876.253696] SLOW spr round 18 (radius: 15) [01:14:07 -49876.253696] SLOW spr round 19 (radius: 20) [01:15:17] [worker #2] ML tree search #3, logLikelihood: -49877.171603 [01:18:03 -49876.253696] SLOW spr round 20 (radius: 25) [01:23:06 -49876.253696] Model parameter optimization (eps = 0.100000) [01:23:16] [worker #0] ML tree search #1, logLikelihood: -49876.052211 [01:23:16 -276682.657055] Initial branch length optimization [01:23:21 -223745.241136] Model parameter optimization (eps = 10.000000) [01:23:58 -223252.538966] AUTODETECT spr round 1 (radius: 5) [01:26:26 -135461.963166] AUTODETECT spr round 2 (radius: 10) [01:28:54 -94776.613042] AUTODETECT spr round 3 (radius: 15) [01:31:30 -76552.209598] AUTODETECT spr round 4 (radius: 20) [01:34:20 -69758.891234] AUTODETECT spr round 5 (radius: 25) [01:37:09 -63710.848887] SPR radius for FAST iterations: 25 (autodetect) [01:37:09 -63710.848887] Model parameter optimization (eps = 3.000000) [01:37:33 -63617.321801] FAST spr round 1 (radius: 25) [01:40:02 -51449.486001] FAST spr round 2 (radius: 25) [01:41:54 -50007.828694] FAST spr round 3 (radius: 25) [01:43:34 -49912.799918] FAST spr round 4 (radius: 25) [01:45:08 -49899.843405] FAST spr round 5 (radius: 25) [01:46:36 -49895.730511] FAST spr round 6 (radius: 25) [01:48:02 -49895.730356] Model parameter optimization (eps = 1.000000) [01:48:14 -49893.152482] SLOW spr round 1 (radius: 5) [01:50:04 -49870.643808] SLOW spr round 2 (radius: 5) [01:51:52 -49867.257273] SLOW spr round 3 (radius: 5) [01:53:42 -49864.880619] SLOW spr round 4 (radius: 5) [01:55:26 -49864.681449] SLOW spr round 5 (radius: 5) [01:57:10 -49864.681339] SLOW spr round 6 (radius: 10) [01:58:58 -49862.511704] SLOW spr round 7 (radius: 5) [02:01:06 -49862.511611] SLOW spr round 8 (radius: 10) [02:03:04 -49862.511578] SLOW spr round 9 (radius: 15) [02:05:25 -49862.511545] SLOW spr round 10 (radius: 20) [02:08:32 -49862.511512] SLOW spr round 11 (radius: 25) [02:12:21 -49862.511477] Model parameter optimization (eps = 0.100000) [02:12:25] [worker #0] ML tree search #4, logLikelihood: -49862.486404 [02:12:25 -275598.700329] Initial branch length optimization [02:12:29 -221148.963260] Model parameter optimization (eps = 10.000000) [02:13:02 -220664.862018] AUTODETECT spr round 1 (radius: 5) [02:13:12] [worker #1] ML tree search #5, logLikelihood: -49871.078564 [02:15:12 -136172.547060] AUTODETECT spr round 2 (radius: 10) [02:17:23 -98166.279576] AUTODETECT spr round 3 (radius: 15) [02:19:37 -79608.198782] AUTODETECT spr round 4 (radius: 20) [02:22:10 -68268.247195] AUTODETECT spr round 5 (radius: 25) [02:24:43 -62092.860608] SPR radius for FAST iterations: 25 (autodetect) [02:24:43 -62092.860608] Model parameter optimization (eps = 3.000000) [02:25:02 -62038.262860] FAST spr round 1 (radius: 25) [02:25:10] [worker #2] ML tree search #6, logLikelihood: -49886.295830 [02:27:25 -51441.133704] FAST spr round 2 (radius: 25) [02:29:22 -50137.779623] FAST spr round 3 (radius: 25) [02:31:04 -49974.080296] FAST spr round 4 (radius: 25) [02:32:38 -49960.752656] FAST spr round 5 (radius: 25) [02:34:08 -49960.142916] FAST spr round 6 (radius: 25) [02:35:35 -49959.152013] FAST spr round 7 (radius: 25) [02:37:02 -49959.151617] Model parameter optimization (eps = 1.000000) [02:37:19 -49914.483016] SLOW spr round 1 (radius: 5) [02:39:07 -49885.648252] SLOW spr round 2 (radius: 5) [02:40:58 -49879.407641] SLOW spr round 3 (radius: 5) [02:42:47 -49879.240298] SLOW spr round 4 (radius: 5) [02:44:34 -49879.240177] SLOW spr round 5 (radius: 10) [02:46:27 -49876.765030] SLOW spr round 6 (radius: 5) [02:48:41 -49874.664261] SLOW spr round 7 (radius: 5) [02:50:42 -49872.340857] SLOW spr round 8 (radius: 5) [02:52:32 -49872.313801] SLOW spr round 9 (radius: 10) [02:54:23 -49872.168023] SLOW spr round 10 (radius: 5) [02:56:34 -49869.604212] SLOW spr round 11 (radius: 5) [02:58:30 -49869.603703] SLOW spr round 12 (radius: 10) [03:00:21 -49869.603616] SLOW spr round 13 (radius: 15) [03:02:51 -49869.008906] SLOW spr round 14 (radius: 5) [03:05:07 -49869.008825] SLOW spr round 15 (radius: 10) [03:06:21] [worker #1] ML tree search #8, logLikelihood: -49881.210264 [03:07:10 -49869.008743] SLOW spr round 16 (radius: 15) [03:09:36 -49869.008665] SLOW spr round 17 (radius: 20) [03:12:54 -49869.008586] SLOW spr round 18 (radius: 25) [03:16:45 -49869.008505] Model parameter optimization (eps = 0.100000) [03:16:50] [worker #0] ML tree search #7, logLikelihood: -49868.939929 [03:16:50 -277509.532535] Initial branch length optimization [03:16:54 -222775.193704] Model parameter optimization (eps = 10.000000) [03:17:34 -222258.397248] AUTODETECT spr round 1 (radius: 5) [03:19:45 -134697.882683] AUTODETECT spr round 2 (radius: 10) [03:22:01 -94275.307548] AUTODETECT spr round 3 (radius: 15) [03:23:30] [worker #2] ML tree search #9, logLikelihood: -49892.030872 [03:24:28 -73363.644749] AUTODETECT spr round 4 (radius: 20) [03:27:01 -67374.138451] AUTODETECT spr round 5 (radius: 25) [03:29:54 -65631.150509] SPR radius for FAST iterations: 25 (autodetect) [03:29:54 -65631.150509] Model parameter optimization (eps = 3.000000) [03:30:12 -65607.358859] FAST spr round 1 (radius: 25) [03:32:37 -57174.443138] FAST spr round 2 (radius: 25) [03:34:40 -56627.282889] FAST spr round 3 (radius: 25) [03:36:31 -56538.898783] FAST spr round 4 (radius: 25) [03:38:14 -56528.495210] FAST spr round 5 (radius: 25) [03:39:52 -56526.057303] FAST spr round 6 (radius: 25) [03:41:26 -56526.056768] Model parameter optimization (eps = 1.000000) [03:41:46 -56512.271861] SLOW spr round 1 (radius: 5) [03:43:44 -56483.246495] SLOW spr round 2 (radius: 5) [03:45:44 -56473.143234] SLOW spr round 3 (radius: 5) [03:47:44 -56472.043852] SLOW spr round 4 (radius: 5) [03:49:42 -56472.043501] SLOW spr round 5 (radius: 10) [03:51:41 -56471.136590] SLOW spr round 6 (radius: 5) [03:54:05 -56471.136535] SLOW spr round 7 (radius: 10) [03:56:14 -56468.963819] SLOW spr round 8 (radius: 5) [03:58:34 -56468.963698] SLOW spr round 9 (radius: 10) [04:00:20] [worker #1] ML tree search #11, logLikelihood: -49870.336985 [04:00:40 -56468.963693] SLOW spr round 10 (radius: 15) [04:03:23 -56468.479517] SLOW spr round 11 (radius: 5) [04:05:53 -56468.479430] SLOW spr round 12 (radius: 10) [04:08:08 -56468.479428] SLOW spr round 13 (radius: 15) [04:10:48 -56468.479425] SLOW spr round 14 (radius: 20) [04:14:23 -56468.479423] SLOW spr round 15 (radius: 25) [04:18:20 -56468.479420] Model parameter optimization (eps = 0.100000) [04:18:30] [worker #0] ML tree search #10, logLikelihood: -56468.254722 [04:18:30 -275139.090268] Initial branch length optimization [04:18:35 -221997.576476] Model parameter optimization (eps = 10.000000) [04:19:16 -221517.047994] AUTODETECT spr round 1 (radius: 5) [04:21:35 -136870.825861] AUTODETECT spr round 2 (radius: 10) [04:23:52 -98988.228941] AUTODETECT spr round 3 (radius: 15) [04:25:56] [worker #2] ML tree search #12, logLikelihood: -49888.999671 [04:26:23 -74823.104477] AUTODETECT spr round 4 (radius: 20) [04:29:01 -66821.863645] AUTODETECT spr round 5 (radius: 25) [04:31:57 -60074.143835] SPR radius for FAST iterations: 25 (autodetect) [04:31:57 -60074.143835] Model parameter optimization (eps = 3.000000) [04:32:20 -59977.500982] FAST spr round 1 (radius: 25) [04:34:40 -50558.205584] FAST spr round 2 (radius: 25) [04:36:32 -50009.528797] FAST spr round 3 (radius: 25) [04:38:17 -49929.379976] FAST spr round 4 (radius: 25) [04:39:56 -49919.241895] FAST spr round 5 (radius: 25) [04:41:25 -49916.472284] FAST spr round 6 (radius: 25) [04:42:54 -49916.472264] Model parameter optimization (eps = 1.000000) [04:43:04 -49912.889594] SLOW spr round 1 (radius: 5) [04:45:01 -49893.443728] SLOW spr round 2 (radius: 5) [04:46:57 -49891.165280] SLOW spr round 3 (radius: 5) [04:48:50 -49890.189484] SLOW spr round 4 (radius: 5) [04:50:40 -49890.189464] SLOW spr round 5 (radius: 10) [04:52:35 -49887.330252] SLOW spr round 6 (radius: 5) [04:54:55 -49887.329533] SLOW spr round 7 (radius: 10) [04:57:02 -49887.003056] SLOW spr round 8 (radius: 5) [04:59:19 -49887.002790] SLOW spr round 9 (radius: 10) [05:01:21 -49887.002765] SLOW spr round 10 (radius: 15) [05:03:54 -49887.002745] SLOW spr round 11 (radius: 20) [05:07:21 -49885.883681] SLOW spr round 12 (radius: 5) [05:09:49 -49885.883599] SLOW spr round 13 (radius: 10) [05:12:03 -49885.883579] SLOW spr round 14 (radius: 15) [05:12:23] [worker #1] ML tree search #14, logLikelihood: -49903.270951 [05:14:33 -49885.883558] SLOW spr round 15 (radius: 20) [05:18:00 -49885.883536] SLOW spr round 16 (radius: 25) [05:20:55] [worker #2] ML tree search #15, logLikelihood: -49889.994541 [05:22:11 -49885.883515] Model parameter optimization (eps = 0.100000) [05:22:16] [worker #0] ML tree search #13, logLikelihood: -49885.855464 [05:22:16 -275924.114443] Initial branch length optimization [05:22:19 -221415.399563] Model parameter optimization (eps = 10.000000) [05:22:48 -220985.949840] AUTODETECT spr round 1 (radius: 5) [05:25:04 -133448.554021] AUTODETECT spr round 2 (radius: 10) [05:27:23 -95188.784743] AUTODETECT spr round 3 (radius: 15) [05:29:49 -80353.508749] AUTODETECT spr round 4 (radius: 20) [05:32:39 -67542.484667] AUTODETECT spr round 5 (radius: 25) [05:35:38 -64063.890758] SPR radius for FAST iterations: 25 (autodetect) [05:35:38 -64063.890758] Model parameter optimization (eps = 3.000000) [05:35:44 -64058.738360] FAST spr round 1 (radius: 25) [05:38:16 -52241.090619] FAST spr round 2 (radius: 25) [05:40:17 -50228.980556] FAST spr round 3 (radius: 25) [05:42:08 -50006.300183] FAST spr round 4 (radius: 25) [05:43:49 -49988.213823] FAST spr round 5 (radius: 25) [05:45:25 -49985.311499] FAST spr round 6 (radius: 25) [05:46:57 -49985.311196] Model parameter optimization (eps = 1.000000) [05:47:17 -49916.854849] SLOW spr round 1 (radius: 5) [05:49:16 -49886.086804] SLOW spr round 2 (radius: 5) [05:51:13 -49885.368816] SLOW spr round 3 (radius: 5) [05:53:05 -49885.368765] SLOW spr round 4 (radius: 10) [05:55:01 -49881.340537] SLOW spr round 5 (radius: 5) [05:57:19 -49881.340507] SLOW spr round 6 (radius: 10) [05:59:26 -49881.340485] SLOW spr round 7 (radius: 15) [06:01:58 -49881.340463] SLOW spr round 8 (radius: 20) [06:05:12 -49881.340441] SLOW spr round 9 (radius: 25) [06:09:15 -49880.998540] SLOW spr round 10 (radius: 5) [06:11:51 -49880.998517] SLOW spr round 11 (radius: 10) [06:14:27 -49880.998493] SLOW spr round 12 (radius: 15) [06:16:01] [worker #2] ML tree search #18, logLikelihood: -49858.843341 [06:17:14 -49880.998469] SLOW spr round 13 (radius: 20) [06:20:53 -49880.998445] SLOW spr round 14 (radius: 25) [06:25:21 -49880.998420] Model parameter optimization (eps = 0.100000) [06:25:29] [worker #0] ML tree search #16, logLikelihood: -49880.845765 [06:25:29 -276204.241765] Initial branch length optimization [06:25:34 -223258.370733] Model parameter optimization (eps = 10.000000) [06:26:17 -222740.458898] AUTODETECT spr round 1 (radius: 5) [06:28:54 -135357.763840] AUTODETECT spr round 2 (radius: 10) [06:31:31 -98960.955279] AUTODETECT spr round 3 (radius: 15) [06:34:15 -77477.103478] AUTODETECT spr round 4 (radius: 20) [06:37:15 -67394.512771] AUTODETECT spr round 5 (radius: 25) [06:37:34] [worker #1] ML tree search #17, logLikelihood: -49884.644584 [06:40:55 -59932.390478] SPR radius for FAST iterations: 25 (autodetect) [06:40:55 -59932.390478] Model parameter optimization (eps = 3.000000) [06:41:19 -59862.814003] FAST spr round 1 (radius: 25) [06:44:10 -51014.242845] FAST spr round 2 (radius: 25) [06:46:26 -50213.324424] FAST spr round 3 (radius: 25) [06:48:29 -50019.404635] FAST spr round 4 (radius: 25) [06:50:26 -49975.686831] FAST spr round 5 (radius: 25) [06:52:14 -49965.030496] FAST spr round 6 (radius: 25) [06:53:58 -49965.030442] Model parameter optimization (eps = 1.000000) [06:54:16 -49962.579718] SLOW spr round 1 (radius: 5) [06:56:25 -49947.569457] SLOW spr round 2 (radius: 5) [06:58:35 -49945.958981] SLOW spr round 3 (radius: 5) [07:00:45 -49944.950329] SLOW spr round 4 (radius: 5) [07:02:53 -49944.950113] SLOW spr round 5 (radius: 10) [07:05:02 -49941.371575] SLOW spr round 6 (radius: 5) [07:07:36 -49941.371338] SLOW spr round 7 (radius: 10) [07:09:57 -49941.371306] SLOW spr round 8 (radius: 15) [07:12:48 -49941.371295] SLOW spr round 9 (radius: 20) [07:16:37 -49941.371289] SLOW spr round 10 (radius: 25) [07:21:28 -49941.371285] Model parameter optimization (eps = 0.100000) [07:21:36] [worker #0] ML tree search #19, logLikelihood: -49941.267657 [07:33:36] [worker #1] ML tree search #20, logLikelihood: -49882.874071 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.176250,0.545484) (0.221214,0.405829) (0.369875,1.004693) (0.232660,1.901795) 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: -49858.843341 AIC score: 103727.686683 / AICc score: 8147787.686683 / BIC score: 109942.918871 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=164). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 340 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75838/3_mltree/O75838.raxml.log Analysis started: 30-Jun-2021 22:44:43 / finished: 01-Jul-2021 06:18:20 Elapsed time: 27216.850 seconds Consumed energy: 2205.160 Wh (= 11 km in an electric car, or 55 km with an e-scooter!)