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 01-Jul-2021 01:46:24 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/2_msa/P29992_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992 --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/P29992/2_msa/P29992_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 349 sites WARNING: Sequences tr_B4QDD9_B4QDD9_DROSI_7240 and tr_B4HPL5_B4HPL5_DROSE_7238 are exactly identical! WARNING: Sequences tr_E9GJ31_E9GJ31_DAPPU_6669 and tr_A0A164WFI7_A0A164WFI7_9CRUS_35525 are exactly identical! WARNING: Sequences tr_Q71RI7_Q71RI7_CHICK_9031 and sp_P45645_GNA11_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q71RI7_Q71RI7_CHICK_9031 and tr_A0A218UGK5_A0A218UGK5_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q71RI7_Q71RI7_CHICK_9031 and tr_A0A226NI77_A0A226NI77_COLVI_9014 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_M3Z3L1_M3Z3L1_MUSPF_9669 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_G3QYF3_G3QYF3_GORGO_9595 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and sp_P63096_GNAI1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_G3TPI4_G3TPI4_LOXAF_9785 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_F1SB90_F1SB90_PIG_9823 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and sp_P63097_GNAI1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_M3W792_M3W792_FELCA_9685 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A0D9RHH6_A0A0D9RHH6_CHLSB_60711 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A1S3AKH7_A0A1S3AKH7_ERIEU_9365 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A1U7U5W0_A0A1U7U5W0_TARSY_1868482 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A2U4BS95_A0A2U4BS95_TURTR_9739 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A2Y9DVT4_A0A2Y9DVT4_TRIMA_127582 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A2Y9KDF4_A0A2Y9KDF4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A2Y9F3S1_A0A2Y9F3S1_PHYCD_9755 are exactly identical! WARNING: Sequences sp_B2RSH2_GNAI1_MOUSE_10090 and tr_A0A384AIK2_A0A384AIK2_BALAS_310752 are exactly identical! WARNING: Sequences sp_P21279_GNAQ_MOUSE_10090 and tr_A0A1U7Q621_A0A1U7Q621_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YMA2_M3YMA2_MUSPF_9669 and tr_W5PS49_W5PS49_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YMA2_M3YMA2_MUSPF_9669 and tr_A0A0D9R5U9_A0A0D9R5U9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YMA2_M3YMA2_MUSPF_9669 and tr_A0A384A538_A0A384A538_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YNV7_M3YNV7_MUSPF_9669 and tr_Q06AS6_Q06AS6_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YNV7_M3YNV7_MUSPF_9669 and tr_D2HET1_D2HET1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YNV7_M3YNV7_MUSPF_9669 and tr_A0A337SF86_A0A337SF86_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YNV7_M3YNV7_MUSPF_9669 and tr_A0A2Y9N3J0_A0A2Y9N3J0_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YNV7_M3YNV7_MUSPF_9669 and tr_A0A2Y9FHK9_A0A2Y9FHK9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_E3RYK0_E3RYK0_PYRTT_861557 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_B2W6L6_B2W6L6_PYRTR_426418 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_A0A163G8Y3_A0A163G8Y3_DIDRA_5454 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_A0A178B861_A0A178B861_9PLEO_765868 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_Q2PEN1_Q2PEN1_ALTAL_5599 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_A0A1Y2LKS2_A0A1Y2LKS2_EPING_105696 are exactly identical! WARNING: Sequences tr_Q0UDS8_Q0UDS8_PHANO_321614 and tr_A0A2W1HES0_A0A2W1HES0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_H2QMN4_H2QMN4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and sp_P04899_GNAI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_A0A096MUH7_A0A096MUH7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_A0A0D9RPC3_A0A0D9RPC3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_A0A1U7TF75_A0A1U7TF75_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_A0A2K5NXA1_A0A2K5NXA1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R5L7_G1R5L7_NOMLE_61853 and tr_A0A2K6CA70_A0A2K6CA70_MACNE_9545 are exactly identical! WARNING: Sequences tr_B6QCL4_B6QCL4_TALMQ_441960 and tr_A0A093XID8_A0A093XID8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2YU68_A0A2I2YU68_GORGO_9595 and tr_A0A2I3TFM8_A0A2I3TFM8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YU68_A0A2I2YU68_GORGO_9595 and tr_A0A2I2U651_A0A2I2U651_FELCA_9685 are exactly identical! WARNING: Sequences tr_G3QKP4_G3QKP4_GORGO_9595 and tr_A0A2I3TWC5_A0A2I3TWC5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKP4_G3QKP4_GORGO_9595 and tr_A0A2R9C5A3_A0A2R9C5A3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QVV7_G3QVV7_GORGO_9595 and tr_A0A2R9ANZ4_A0A2R9ANZ4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RCJ5_G3RCJ5_GORGO_9595 and tr_H2PSG3_H2PSG3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RCJ5_G3RCJ5_GORGO_9595 and tr_A0A2I3TRC4_A0A2I3TRC4_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and sp_Q28294_GNAQ_CANLF_9615 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_K6ZCJ5_K6ZCJ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_F7G1K7_F7G1K7_MONDO_13616 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_H0X055_H0X055_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and sp_P50148_GNAQ_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_G3W7B2_G3W7B2_SARHA_9305 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_F7IC22_F7IC22_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and sp_Q2PKF4_GNAQ_PIG_9823 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_E1BA29_E1BA29_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_M3XDT0_M3XDT0_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2K5KIT2_A0A2K5KIT2_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2K6BEP2_A0A2K6BEP2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2U4BAF5_A0A2U4BAF5_TURTR_9739 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2U3VP38_A0A2U3VP38_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2Y9K584_A0A2Y9K584_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2Y9NIQ8_A0A2Y9NIQ8_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2PSG4_H2PSG4_PONAB_9601 and tr_A0A2Y9SWK4_A0A2Y9SWK4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3JM92_G3JM92_CORMM_983644 and tr_J4USZ8_J4USZ8_BEAB2_655819 are exactly identical! WARNING: Sequences tr_G3JM92_G3JM92_CORMM_983644 and tr_A0A0A2VQW4_A0A0A2VQW4_BEABA_1245745 are exactly identical! WARNING: Sequences tr_G3JM92_G3JM92_CORMM_983644 and tr_A0A167H2V9_A0A167H2V9_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_F9G3S6_F9G3S6_FUSOF_660025 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_C7YYR0_C7YYR0_NECH7_660122 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_W7MG32_W7MG32_GIBM7_334819 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A0C4DHV0_A0A0C4DHV0_FUSO4_426428 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_S0E9D0_S0E9D0_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_N4UPG3_N4UPG3_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A086SY68_A0A086SY68_ACRC1_857340 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_X0DL30_X0DL30_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A0M9ETN3_A0A0M9ETN3_FUSLA_179993 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A0G4M4R7_A0A0G4M4R7_9PEZI_100787 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_I1RNF9_I1RNF9_GIBZE_229533 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A1B8AL03_A0A1B8AL03_FUSPO_36050 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_Q96VA7_Q96VA7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A2K0WHT8_A0A2K0WHT8_GIBNY_42673 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A2L2TC88_A0A2L2TC88_9HYPO_56646 are exactly identical! WARNING: Sequences tr_G2X6F0_G2X6F0_VERDV_498257 and tr_A0A365MWM1_A0A365MWM1_GIBIN_948311 are exactly identical! WARNING: Sequences sp_Q05425_GPA1_NEUCR_367110 and tr_G4UN29_G4UN29_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q28YH5_Q28YH5_DROPS_46245 and tr_B4H8L7_B4H8L7_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1PXM5_F1PXM5_CANLF_9615 and tr_A0A384C2T8_A0A384C2T8_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2QEY0_H2QEY0_PANTR_9598 and sp_P29992_GNA11_HUMAN_9606 are exactly identical! WARNING: Sequences tr_W5PKD3_W5PKD3_SHEEP_9940 and tr_A7MBH9_A7MBH9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_E9ETY9_E9ETY9_METRA_655844 and tr_E9E5A8_E9E5A8_METAQ_655827 are exactly identical! WARNING: Sequences tr_E9ETY9_E9ETY9_METRA_655844 and tr_A0A0B2X604_A0A0B2X604_METAS_1081103 are exactly identical! WARNING: Sequences tr_E9ETY9_E9ETY9_METRA_655844 and tr_A0A0D9NSF3_A0A0D9NSF3_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9ETY9_E9ETY9_METRA_655844 and tr_A0A167F3U2_A0A167F3U2_9HYPO_1081105 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A1D2A6_A1D2A6_NEOFI_331117 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A0A0K8LN39_A0A0K8LN39_9EURO_91492 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A0A0S7E7A7_A0A0S7E7A7_9EURO_293939 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A0A229XFH4_A0A229XFH4_9EURO_1245748 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A0A397H8Z7_A0A397H8Z7_9EURO_41047 are exactly identical! WARNING: Sequences tr_E9QVH0_E9QVH0_ASPFU_330879 and tr_A0A2I1C8V2_A0A2I1C8V2_9EURO_1392255 are exactly identical! WARNING: Sequences tr_E4USW2_E4USW2_ARTGP_535722 and tr_F2PN52_F2PN52_TRIEC_559882 are exactly identical! WARNING: Sequences tr_E4USW2_E4USW2_ARTGP_535722 and tr_A0A059IYL1_A0A059IYL1_9EURO_1215338 are exactly identical! WARNING: Sequences tr_A0A3B5PWN0_A0A3B5PWN0_XIPMA_8083 and tr_A0A087YFW3_A0A087YFW3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZWN8_A0A087ZWN8_APIME_7460 and tr_A0A2A3E6D2_A0A2A3E6D2_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158P1D3_A0A158P1D3_ATTCE_12957 and tr_F4X7J7_F4X7J7_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P1D3_A0A158P1D3_ATTCE_12957 and tr_A0A195EY86_A0A195EY86_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3MUA0_I3MUA0_ICTTR_43179 and tr_A0A286XMK5_A0A286XMK5_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G9NUI4_G9NUI4_HYPAI_452589 and tr_A0A0W7W0U4_A0A0W7W0U4_9HYPO_398673 are exactly identical! WARNING: Sequences tr_Q2UCI4_Q2UCI4_ASPOR_510516 and tr_A0A0F0IEH7_A0A0F0IEH7_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_Q2UCI4_Q2UCI4_ASPOR_510516 and tr_A0A1S9DQE3_A0A1S9DQE3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UCI4_Q2UCI4_ASPOR_510516 and tr_A0A2G7G9Q5_A0A2G7G9Q5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0J9Y4U4_A0A0J9Y4U4_BRUMA_6279 and tr_A0A158PPV9_A0A158PPV9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_G7XNI1_G7XNI1_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_G3YHH3_G3YHH3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_A0A100IIH6_A0A100IIH6_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_A0A1L9NP10_A0A1L9NP10_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_A0A1L9UPM5_A0A1L9UPM5_9EURO_767769 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_A0A317W573_A0A317W573_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2QRI2_A2QRI2_ASPNC_425011 and tr_A0A319AHB3_A0A319AHB3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A1D5QG31_A0A1D5QG31_MACMU_9544 and tr_G7PYJ3_G7PYJ3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QG31_A0A1D5QG31_MACMU_9544 and tr_A0A0A0MWA0_A0A0A0MWA0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AQR3_F7AQR3_MACMU_9544 and tr_G7PSK6_G7PSK6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AQR3_F7AQR3_MACMU_9544 and tr_A0A2K6DHZ6_A0A2K6DHZ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V0RP25_A0A0V0RP25_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V1CNM8_A0A0V1CNM8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V0WKF4_A0A0V0WKF4_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V0UYB7_A0A0V0UYB7_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V1L9H9_A0A0V1L9H9_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V0ZSQ6_A0A0V0ZSQ6_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V1MES3_A0A0V1MES3_9BILA_268474 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V1NRA1_A0A0V1NRA1_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V1HK07_A0A0V1HK07_9BILA_268475 are exactly identical! WARNING: Sequences tr_E5SUB9_E5SUB9_TRISP_6334 and tr_A0A0V0UBC8_A0A0V0UBC8_9BILA_144512 are exactly identical! WARNING: Sequences tr_G9N3B7_G9N3B7_HYPVG_413071 and tr_G0RRW6_G0RRW6_HYPJQ_431241 are exactly identical! WARNING: Sequences tr_G9N3B7_G9N3B7_HYPVG_413071 and tr_H6VTT1_H6VTT1_TRIHA_5544 are exactly identical! WARNING: Sequences tr_G9N3B7_G9N3B7_HYPVG_413071 and tr_A0A2T3Z9B4_A0A2T3Z9B4_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_G9N3B7_G9N3B7_HYPVG_413071 and tr_A0A2T4BEV0_A0A2T4BEV0_9HYPO_58853 are exactly identical! WARNING: Sequences tr_G9N3B7_G9N3B7_HYPVG_413071 and tr_A0A2T3ZZC0_A0A2T3ZZC0_TRIHA_983964 are exactly identical! WARNING: Sequences tr_F4P8M9_F4P8M9_BATDJ_684364 and tr_A0A177WU44_A0A177WU44_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_U3KHJ2_U3KHJ2_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_U3I8L6_U3I8L6_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A091FU18_A0A091FU18_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A091J0V8_A0A091J0V8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A091VEG2_A0A091VEG2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A087R386_A0A087R386_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A091WKA7_A0A091WKA7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A091FKA5_A0A091FKA5_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0YQK2_H0YQK2_TAEGU_59729 and tr_A0A0A0B3Q8_A0A0A0B3Q8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0YSB0_H0YSB0_TAEGU_59729 and tr_A0A218URS7_A0A218URS7_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0YYZ8_H0YYZ8_TAEGU_59729 and tr_A0A218UPT8_A0A218UPT8_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0Q9X0Z5_A0A0Q9X0Z5_DROWI_7260 and tr_A0A0P8XRN2_A0A0P8XRN2_DROAN_7217 are exactly identical! WARNING: Sequences tr_A0A0Q9X0Z5_A0A0Q9X0Z5_DROWI_7260 and tr_A0A1W4VQ13_A0A1W4VQ13_DROFC_30025 are exactly identical! WARNING: Sequences tr_F9WWH9_F9WWH9_ZYMTI_336722 and tr_A0A0F4GVG6_A0A0F4GVG6_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9WWH9_F9WWH9_ZYMTI_336722 and tr_A0A1X7REB4_A0A1X7REB4_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F7A472_F7A472_XENTR_8364 and tr_A0A1L8GTV0_A0A1L8GTV0_XENLA_8355 are exactly identical! WARNING: Sequences tr_E3LXV8_E3LXV8_CAERE_31234 and tr_A8Y1T0_A8Y1T0_CAEBR_6238 are exactly identical! WARNING: Sequences tr_E3LXV8_E3LXV8_CAERE_31234 and tr_A0A261B5L1_A0A261B5L1_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3LXV8_E3LXV8_CAERE_31234 and tr_A0A2G5VU95_A0A2G5VU95_9PELO_1611254 are exactly identical! WARNING: Sequences tr_E3Q2X0_E3Q2X0_COLGM_645133 and tr_N4UTV4_N4UTV4_COLOR_1213857 are exactly identical! WARNING: Sequences tr_F2SZ62_F2SZ62_TRIRC_559305 and tr_A0A178F480_A0A178F480_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G7PYJ4_G7PYJ4_MACFA_9541 and tr_A0A2K6DJ24_A0A2K6DJ24_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PYJ4_G7PYJ4_MACFA_9541 and tr_A0A2K5YUW3_A0A2K5YUW3_MANLE_9568 are exactly identical! WARNING: Sequences sp_P38409_GNA11_BOVIN_9913 and tr_A0A2Y9TKW2_A0A2Y9TKW2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A0A2KA44_A0A0A2KA44_PENEN_27334 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_W6PXS3_W6PXS3_PENRF_1365484 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A0M8P1C6_A0A0M8P1C6_9EURO_229535 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A0G4P8P2_A0A0G4P8P2_PENCA_1429867 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A117NKJ2_A0A117NKJ2_9EURO_48697 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A1V6N9K6_A0A1V6N9K6_9EURO_60169 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A1V6RG07_A0A1V6RG07_9EURO_29845 are exactly identical! WARNING: Sequences tr_K9FDI4_K9FDI4_PEND2_1170229 and tr_A0A1V6R1Q0_A0A1V6R1Q0_9EURO_60172 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_T0L1K0_T0L1K0_COLGC_1237896 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A010Q1Z8_A0A010Q1Z8_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A066XBF5_A0A066XBF5_COLSU_1173701 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A135UES9_A0A135UES9_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A166NW83_A0A166NW83_9PEZI_708197 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A161Y974_A0A161Y974_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_L2G133_L2G133_COLFN_1213859 and tr_A0A1Q8RB89_A0A1Q8RB89_9PEZI_708187 are exactly identical! WARNING: Sequences tr_A0A337S5X4_A0A337S5X4_FELCA_9685 and tr_A0A2U3YMA5_A0A2U3YMA5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A337S5X4_A0A337S5X4_FELCA_9685 and tr_A0A2Y9L8E2_A0A2Y9L8E2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3JJU1_U3JJU1_FICAL_59894 and tr_A0A218USS0_A0A218USS0_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K2E5_U3K2E5_FICAL_59894 and tr_A0A218VBV5_A0A218VBV5_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K7B8_U3K7B8_FICAL_59894 and tr_A0A218URG2_A0A218URG2_9PASE_299123 are exactly identical! WARNING: Sequences tr_M2UIQ7_M2UIQ7_COCH5_701091 and tr_W6YDG1_W6YDG1_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2UIQ7_M2UIQ7_COCH5_701091 and tr_W6ZIX2_W6ZIX2_COCMI_930090 are exactly identical! WARNING: Sequences tr_W9VYU0_W9VYU0_9EURO_1182543 and tr_A0A0D2BV37_A0A0D2BV37_9EURO_569365 are exactly identical! WARNING: Sequences tr_A0A015IHM6_A0A015IHM6_9GLOM_1432141 and tr_U9UBM6_U9UBM6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015IWQ7_A0A015IWQ7_9GLOM_1432141 and tr_A0A2H5S2F5_A0A2H5S2F5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A074XAB8_A0A074XAB8_9PEZI_1043004 and tr_A0A074VEA9_A0A074VEA9_9PEZI_1043003 are exactly identical! WARNING: Sequences tr_A0A074XAB8_A0A074XAB8_9PEZI_1043004 and tr_A0A074XPR2_A0A074XPR2_AURPU_1043002 are exactly identical! WARNING: Sequences tr_A0A096P1U3_A0A096P1U3_PAPAN_9555 and tr_A0A2K5KIZ8_A0A2K5KIZ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P1U3_A0A096P1U3_PAPAN_9555 and tr_A0A2K5YHR9_A0A2K5YHR9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094E0D0_A0A094E0D0_9PEZI_1420912 and tr_A0A1B8EFT1_A0A1B8EFT1_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094E0D0_A0A094E0D0_9PEZI_1420912 and tr_A0A1B8GDT0_A0A1B8GDT0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094E0D0_A0A094E0D0_9PEZI_1420912 and tr_A0A1B8CFW3_A0A1B8CFW3_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094E0D0_A0A094E0D0_9PEZI_1420912 and tr_A0A1B8FAG5_A0A1B8FAG5_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0F8U573_A0A0F8U573_9EURO_308745 and tr_A0A2T5M3Q1_A0A2T5M3Q1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0G2H8Q5_A0A0G2H8Q5_9PEZI_1214573 and tr_A0A2P5IBY7_A0A2P5IBY7_9PEZI_158607 are exactly identical! WARNING: Sequences tr_A0A0K0F8J0_A0A0K0F8J0_STRVS_75913 and tr_A0A0K0EBP3_A0A0K0EBP3_STRER_6248 are exactly identical! WARNING: Sequences tr_A0A0K0F8J0_A0A0K0F8J0_STRVS_75913 and tr_A0A090LBM0_A0A090LBM0_STRRB_34506 are exactly identical! WARNING: Sequences tr_A0A0K0F8J0_A0A0K0F8J0_STRVS_75913 and tr_A0A0N5BWB1_A0A0N5BWB1_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0L1IPY9_A0A0L1IPY9_ASPNO_1509407 and tr_A0A1F8AAV6_A0A1F8AAV6_9EURO_109264 are exactly identical! WARNING: Sequences tr_A0A0D2D9V6_A0A0D2D9V6_9EURO_1442368 and tr_A0A0D2K7N9_A0A0D2K7N9_9EURO_1442371 are exactly identical! WARNING: Sequences tr_A0A091J494_A0A091J494_EGRGA_188379 and tr_A0A091WEM4_A0A091WEM4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091J494_A0A091J494_EGRGA_188379 and tr_A0A091G0E9_A0A091G0E9_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091J494_A0A091J494_EGRGA_188379 and tr_A0A099ZX61_A0A099ZX61_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093Q6H1_A0A093Q6H1_9PASS_328815 and tr_A0A093HYI1_A0A093HYI1_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A093Q6H1_A0A093Q6H1_9PASS_328815 and tr_A0A099YZ67_A0A099YZ67_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A093Q6H1_A0A093Q6H1_9PASS_328815 and tr_A0A093I4H2_A0A093I4H2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V0S1J1_A0A0V0S1J1_9BILA_6336 and tr_A0A0V0TPW0_A0A0V0TPW0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CIS9_A0A0V1CIS9_TRIBR_45882 and tr_A0A0V0WEY0_A0A0V0WEY0_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CIS9_A0A0V1CIS9_TRIBR_45882 and tr_A0A0V1LFY6_A0A0V1LFY6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CIS9_A0A0V1CIS9_TRIBR_45882 and tr_A0A0V1IHH7_A0A0V1IHH7_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V1CIS9_A0A0V1CIS9_TRIBR_45882 and tr_A0A0V1MZT8_A0A0V1MZT8_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1CIS9_A0A0V1CIS9_TRIBR_45882 and tr_A0A0V1HI09_A0A0V1HI09_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A195DTQ4_A0A195DTQ4_9HYME_471704 and tr_A0A195BKE6_A0A195BKE6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1S3LSY5_A0A1S3LSY5_SALSA_8030 and tr_A0A060XG16_A0A060XG16_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7UE76_A0A1I7UE76_9PELO_1561998 and tr_A0A1I7UE77_A0A1I7UE77_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1L9P5S2_A0A1L9P5S2_ASPVE_1036611 and tr_A0A1L9TTL7_A0A1L9TTL7_9EURO_1036612 are exactly identical! WARNING: Sequences tr_A0A1L9X8L6_A0A1L9X8L6_ASPAC_690307 and tr_A0A319DHW3_A0A319DHW3_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9X8L6_A0A1L9X8L6_ASPAC_690307 and tr_A0A318ZLD2_A0A318ZLD2_9EURO_1450539 are exactly identical! WARNING: Sequences tr_A0A1L9X8L6_A0A1L9X8L6_ASPAC_690307 and tr_A0A2V5IB59_A0A2V5IB59_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9X8L6_A0A1L9X8L6_ASPAC_690307 and tr_A0A395HI38_A0A395HI38_9EURO_1450537 are exactly identical! WARNING: Sequences tr_A0A1L9X8L6_A0A1L9X8L6_ASPAC_690307 and tr_A0A2V5HI40_A0A2V5HI40_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A1R3S1Z6_A0A1R3S1Z6_ASPC5_602072 and tr_A0A317XE52_A0A317XE52_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A1R3S1Z6_A0A1R3S1Z6_ASPC5_602072 and tr_A0A319EGT3_A0A319EGT3_9EURO_1448318 are exactly identical! WARNING: Sequences tr_A0A1R3S1Z6_A0A1R3S1Z6_ASPC5_602072 and tr_A0A395GT55_A0A395GT55_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A2H3IIH6_A0A2H3IIH6_9EURO_290292 and tr_A0A364KRC9_A0A364KRC9_9EURO_1196081 are exactly identical! WARNING: Sequences tr_A0A2D0RUI8_A0A2D0RUI8_ICTPU_7998 and tr_A0A2D0RUI9_A0A2D0RUI9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G5I9H4_A0A2G5I9H4_CERBT_122368 and tr_A0A2I0RLZ5_A0A2I0RLZ5_9PEZI_348901 are exactly identical! WARNING: Sequences tr_A0A2G5I9H4_A0A2G5I9H4_CERBT_122368 and tr_A0A2S6C2G4_A0A2S6C2G4_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2K5Y295_A0A2K5Y295_MANLE_9568 and tr_A0A2R9A051_A0A2R9A051_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2P7YJ69_A0A2P7YJ69_9PEZI_40998 and tr_A0A2K1QNC4_A0A2K1QNC4_9PEZI_2082308 are exactly identical! WARNING: Sequences tr_A0A2U3VNV5_A0A2U3VNV5_ODORO_9708 and tr_A0A2U3XHR8_A0A2U3XHR8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A369GT28_A0A369GT28_9HYPO_2039875 and tr_A0A367LNS4_A0A367LNS4_9HYPO_1330021 are exactly identical! WARNING: Duplicate sequences found: 237 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/P29992/3_mltree/P29992.raxml.reduced.phy Alignment comprises 1 partitions and 349 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 349 / 349 Gaps: 2.60 % Invariant sites: 1.72 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992.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 -427646.866513] Initial branch length optimization [00:00:10 -337959.149995] Model parameter optimization (eps = 10.000000) [00:01:32 -337192.741679] AUTODETECT spr round 1 (radius: 5) [00:06:04 -188180.327627] AUTODETECT spr round 2 (radius: 10) [00:10:49 -130892.314251] AUTODETECT spr round 3 (radius: 15) [00:15:36 -107559.397990] AUTODETECT spr round 4 (radius: 20) [00:21:14 -97974.840485] AUTODETECT spr round 5 (radius: 25) [00:28:18 -89668.531648] SPR radius for FAST iterations: 25 (autodetect) [00:28:18 -89668.531648] Model parameter optimization (eps = 3.000000) [00:28:53 -89434.093033] FAST spr round 1 (radius: 25) [00:34:08 -71768.425013] FAST spr round 2 (radius: 25) [00:37:39 -70458.181155] FAST spr round 3 (radius: 25) [00:40:30 -70366.199404] FAST spr round 4 (radius: 25) [00:43:14 -70356.873736] FAST spr round 5 (radius: 25) [00:45:40 -70355.145949] FAST spr round 6 (radius: 25) [00:48:01 -70355.145685] Model parameter optimization (eps = 1.000000) [00:48:19 -70351.504368] SLOW spr round 1 (radius: 5) [00:51:39 -70325.801164] SLOW spr round 2 (radius: 5) [00:54:58 -70321.701864] SLOW spr round 3 (radius: 5) [00:58:15 -70313.892331] SLOW spr round 4 (radius: 5) [01:01:22 -70313.892232] SLOW spr round 5 (radius: 10) [01:04:38 -70313.627522] SLOW spr round 6 (radius: 5) [01:08:44 -70313.627432] SLOW spr round 7 (radius: 10) [01:12:33 -70313.627393] SLOW spr round 8 (radius: 15) [01:17:31 -70313.627353] SLOW spr round 9 (radius: 20) [01:24:27 -70313.627022] SLOW spr round 10 (radius: 25) [01:30:56] [worker #4] ML tree search #5, logLikelihood: -70305.479792 [01:32:31] [worker #2] ML tree search #3, logLikelihood: -70336.091295 [01:34:13 -70313.627010] Model parameter optimization (eps = 0.100000) [01:34:24] [worker #0] ML tree search #1, logLikelihood: -70313.477047 [01:34:24 -424561.802476] Initial branch length optimization [01:34:32 -335976.637627] Model parameter optimization (eps = 10.000000) [01:35:55 -335208.623248] AUTODETECT spr round 1 (radius: 5) [01:39:51 -191899.150142] AUTODETECT spr round 2 (radius: 10) [01:44:08 -133874.772949] AUTODETECT spr round 3 (radius: 15) [01:48:22 -105933.542912] AUTODETECT spr round 4 (radius: 20) [01:48:31] [worker #1] ML tree search #2, logLikelihood: -70323.695211 [01:53:25 -92048.857160] AUTODETECT spr round 5 (radius: 25) [01:59:05 -87100.427466] SPR radius for FAST iterations: 25 (autodetect) [01:59:05 -87100.427466] Model parameter optimization (eps = 3.000000) [01:59:38 -86900.647900] FAST spr round 1 (radius: 25) [02:04:15 -71599.979110] FAST spr round 2 (radius: 25) [02:07:11 -70481.289754] FAST spr round 3 (radius: 25) [02:09:47 -70397.013679] FAST spr round 4 (radius: 25) [02:12:10 -70374.260101] FAST spr round 5 (radius: 25) [02:14:17 -70371.186243] FAST spr round 6 (radius: 25) [02:16:18 -70370.591726] FAST spr round 7 (radius: 25) [02:18:16 -70370.591725] Model parameter optimization (eps = 1.000000) [02:18:28 -70369.129743] SLOW spr round 1 (radius: 5) [02:19:04] [worker #3] ML tree search #4, logLikelihood: -70302.038030 [02:21:18 -70357.523512] SLOW spr round 2 (radius: 5) [02:24:07 -70353.358035] SLOW spr round 3 (radius: 5) [02:26:47 -70352.630509] SLOW spr round 4 (radius: 5) [02:29:28 -70352.580570] SLOW spr round 5 (radius: 10) [02:32:20 -70344.519483] SLOW spr round 6 (radius: 5) [02:35:54 -70342.887377] SLOW spr round 7 (radius: 5) [02:39:01 -70342.886850] SLOW spr round 8 (radius: 10) [02:42:02 -70342.886846] SLOW spr round 9 (radius: 15) [02:46:44 -70327.595295] SLOW spr round 10 (radius: 5) [02:50:25 -70323.585136] SLOW spr round 11 (radius: 5) [02:53:32 -70323.585133] SLOW spr round 12 (radius: 10) [02:56:34 -70323.585133] SLOW spr round 13 (radius: 15) [03:01:11 -70323.585133] SLOW spr round 14 (radius: 20) [03:06:43] [worker #4] ML tree search #10, logLikelihood: -70303.517565 [03:07:38 -70323.585133] SLOW spr round 15 (radius: 25) [03:13:19] [worker #2] ML tree search #8, logLikelihood: -70318.531741 [03:16:50 -70323.585132] Model parameter optimization (eps = 0.100000) [03:16:56] [worker #0] ML tree search #6, logLikelihood: -70323.563728 [03:16:57 -425247.144793] Initial branch length optimization [03:17:03 -338208.600601] Model parameter optimization (eps = 10.000000) [03:18:37 -337412.943267] AUTODETECT spr round 1 (radius: 5) [03:22:28 -192654.167509] AUTODETECT spr round 2 (radius: 10) [03:26:35 -135224.673821] AUTODETECT spr round 3 (radius: 15) [03:30:51 -108953.756420] AUTODETECT spr round 4 (radius: 20) [03:33:05] [worker #1] ML tree search #7, logLikelihood: -70310.799229 [03:35:57 -93722.718778] AUTODETECT spr round 5 (radius: 25) [03:38:20] [worker #3] ML tree search #9, logLikelihood: -70301.692543 [03:41:06 -88321.081893] SPR radius for FAST iterations: 25 (autodetect) [03:41:06 -88321.081893] Model parameter optimization (eps = 3.000000) [03:41:39 -88111.736535] FAST spr round 1 (radius: 25) [03:45:34 -74357.684002] FAST spr round 2 (radius: 25) [03:48:26 -72470.961427] FAST spr round 3 (radius: 25) [03:50:57 -70519.930519] FAST spr round 4 (radius: 25) [03:53:13 -70397.086732] FAST spr round 5 (radius: 25) [03:55:30 -70360.111854] FAST spr round 6 (radius: 25) [03:57:37 -70356.595194] FAST spr round 7 (radius: 25) [03:59:36 -70356.595046] Model parameter optimization (eps = 1.000000) [03:59:53 -70352.390339] SLOW spr round 1 (radius: 5) [04:02:43 -70342.348361] SLOW spr round 2 (radius: 5) [04:05:32 -70342.164369] SLOW spr round 3 (radius: 5) [04:08:23 -70340.730309] SLOW spr round 4 (radius: 5) [04:11:15 -70339.671755] SLOW spr round 5 (radius: 5) [04:14:05 -70339.671479] SLOW spr round 6 (radius: 10) [04:16:54 -70339.671406] SLOW spr round 7 (radius: 15) [04:21:40 -70325.040399] SLOW spr round 8 (radius: 5) [04:25:31 -70320.966284] SLOW spr round 9 (radius: 5) [04:28:47 -70320.965874] SLOW spr round 10 (radius: 10) [04:31:56 -70313.756154] SLOW spr round 11 (radius: 5) [04:35:30 -70306.106415] SLOW spr round 12 (radius: 5) [04:36:42] [worker #4] ML tree search #15, logLikelihood: -70305.959723 [04:38:34 -70306.106198] SLOW spr round 13 (radius: 10) [04:41:31 -70306.106106] SLOW spr round 14 (radius: 15) [04:46:11 -70306.106029] SLOW spr round 15 (radius: 20) [04:52:53 -70306.105950] SLOW spr round 16 (radius: 25) [04:55:30] [worker #3] ML tree search #14, logLikelihood: -70327.796879 [05:02:16 -70306.105870] Model parameter optimization (eps = 0.100000) [05:02:24] [worker #0] ML tree search #11, logLikelihood: -70306.069094 [05:02:24 -425385.039489] Initial branch length optimization [05:02:31 -336229.623119] Model parameter optimization (eps = 10.000000) [05:03:57 -335473.542150] AUTODETECT spr round 1 (radius: 5) [05:04:55] [worker #2] ML tree search #13, logLikelihood: -70302.146119 [05:07:47 -195364.916447] AUTODETECT spr round 2 (radius: 10) [05:12:00 -140910.662624] AUTODETECT spr round 3 (radius: 15) [05:16:09 -112642.302098] AUTODETECT spr round 4 (radius: 20) [05:17:00] [worker #1] ML tree search #12, logLikelihood: -70318.968919 [05:20:48 -97667.245692] AUTODETECT spr round 5 (radius: 25) [05:26:16 -93470.657949] SPR radius for FAST iterations: 25 (autodetect) [05:26:16 -93470.657949] Model parameter optimization (eps = 3.000000) [05:26:44 -93244.828199] FAST spr round 1 (radius: 25) [05:30:47 -77799.865694] FAST spr round 2 (radius: 25) [05:33:39 -73006.653577] FAST spr round 3 (radius: 25) [05:36:02 -70956.875819] FAST spr round 4 (radius: 25) [05:38:19 -70501.813064] FAST spr round 5 (radius: 25) [05:40:28 -70420.148489] FAST spr round 6 (radius: 25) [05:42:29 -70416.498673] FAST spr round 7 (radius: 25) [05:44:24 -70416.498520] Model parameter optimization (eps = 1.000000) [05:44:46 -70398.809947] SLOW spr round 1 (radius: 5) [05:47:33 -70377.540615] SLOW spr round 2 (radius: 5) [05:50:18 -70373.989113] SLOW spr round 3 (radius: 5) [05:53:01 -70373.988563] SLOW spr round 4 (radius: 10) [05:55:54 -70372.832368] SLOW spr round 5 (radius: 5) [05:59:25 -70372.832069] SLOW spr round 6 (radius: 10) [06:02:38 -70372.831881] SLOW spr round 7 (radius: 15) [06:07:02 -70353.817755] SLOW spr round 8 (radius: 5) [06:07:51] [worker #3] ML tree search #19, logLikelihood: -70347.225633 [06:10:55 -70306.405097] SLOW spr round 9 (radius: 5) [06:14:10 -70304.158058] SLOW spr round 10 (radius: 5) [06:17:03 -70304.157467] SLOW spr round 11 (radius: 10) [06:19:54 -70304.156926] SLOW spr round 12 (radius: 15) [06:24:20 -70304.156487] SLOW spr round 13 (radius: 20) [06:27:03] [worker #2] ML tree search #18, logLikelihood: -70315.220911 [06:30:44 -70303.513718] SLOW spr round 14 (radius: 5) [06:34:28 -70303.513446] SLOW spr round 15 (radius: 10) [06:38:01 -70303.513354] SLOW spr round 16 (radius: 15) [06:42:16 -70303.513308] SLOW spr round 17 (radius: 20) [06:48:34] [worker #4] ML tree search #20, logLikelihood: -70315.725408 [06:48:58 -70303.263501] SLOW spr round 18 (radius: 5) [06:52:45 -70298.035395] SLOW spr round 19 (radius: 5) [06:55:55 -70298.034940] SLOW spr round 20 (radius: 10) [06:58:52 -70298.027964] SLOW spr round 21 (radius: 15) [07:03:16 -70298.027945] SLOW spr round 22 (radius: 20) [07:09:56 -70298.027937] SLOW spr round 23 (radius: 25) [07:19:15 -70298.027929] Model parameter optimization (eps = 0.100000) [07:19:28] [worker #0] ML tree search #16, logLikelihood: -70297.710069 [07:59:58] [worker #1] ML tree search #17, logLikelihood: -70298.456028 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.277289,0.279485) (0.275818,0.368574) (0.265288,1.049871) (0.181604,2.986294) 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: -70297.710069 AIC score: 144605.420139 / AICc score: 8188665.420139 / BIC score: 152334.839343 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=349). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P29992/3_mltree/P29992.raxml.log Analysis started: 01-Jul-2021 01:46:24 / finished: 01-Jul-2021 09:46:23 Elapsed time: 28798.494 seconds Consumed energy: 2362.892 Wh (= 12 km in an electric car, or 59 km with an e-scooter!)