RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 04-Jul-2021 15:31:42 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/2_msa/Q9ULI4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/2_msa/Q9ULI4_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 205 sites

WARNING: Sequences tr_B4Q5U6_B4Q5U6_DROSI_7240 and tr_B4HYB5_B4HYB5_DROSE_7238 are exactly identical!
WARNING: Sequences tr_E1ZXK1_E1ZXK1_CAMFO_104421 and tr_A0A158NZT6_A0A158NZT6_ATTCE_12957 are exactly identical!
WARNING: Sequences tr_E1ZXK1_E1ZXK1_CAMFO_104421 and tr_F4WIA9_F4WIA9_ACREC_103372 are exactly identical!
WARNING: Sequences tr_E1ZXK1_E1ZXK1_CAMFO_104421 and tr_A0A151WQD7_A0A151WQD7_9HYME_64791 are exactly identical!
WARNING: Sequences tr_E1ZXK1_E1ZXK1_CAMFO_104421 and tr_A0A195BMG4_A0A195BMG4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A2R8QGI2_A0A2R8QGI2_DANRE_7955 and tr_M4A3Y4_M4A3Y4_XIPMA_8083 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_G1NFX3_G1NFX3_MELGA_9103 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_H9GI60_H9GI60_ANOCA_28377 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_F7FCR6_F7FCR6_MONDO_13616 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_G3WR02_G3WR02_SARHA_9305 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_U3IY78_U3IY78_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A091UK25_A0A091UK25_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A093HX90_A0A093HX90_STRCA_441894 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A091WM33_A0A091WM33_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A099Z634_A0A099Z634_TINGU_94827 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A0A0B2X0_A0A0A0B2X0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A091IMV0_A0A091IMV0_CALAN_9244 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A226NH88_A0A226NH88_CALSU_9009 are exactly identical!
WARNING: Sequences tr_E1C4G2_E1C4G2_CHICK_9031 and tr_A0A226PLD1_A0A226PLD1_COLVI_9014 are exactly identical!
WARNING: Sequences tr_F1NW72_F1NW72_CHICK_9031 and tr_G1NL42_G1NL42_MELGA_9103 are exactly identical!
WARNING: Sequences tr_R4GFP1_R4GFP1_CHICK_9031 and tr_G1NMS2_G1NMS2_MELGA_9103 are exactly identical!
WARNING: Sequences tr_R4GFP1_R4GFP1_CHICK_9031 and tr_A0A226MF24_A0A226MF24_CALSU_9009 are exactly identical!
WARNING: Sequences tr_R4GFP1_R4GFP1_CHICK_9031 and tr_A0A226PF49_A0A226PF49_COLVI_9014 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_W5P3I3_W5P3I3_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_D4ADC4_D4ADC4_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_F1S8L6_F1S8L6_PIG_9823 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_G3MZ58_G3MZ58_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_A0A3Q0D2T0_A0A3Q0D2T0_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q7TNC6_KI26B_MOUSE_10090 and tr_A0A2U3VYB3_A0A2U3VYB3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_B6HPF4_B6HPF4_PENRW_500485 and tr_A0A1V6Y9A7_A0A1V6Y9A7_PENNA_60175 are exactly identical!
WARNING: Sequences tr_E3S2B5_E3S2B5_PYRTT_861557 and tr_A0A2W1HKH4_A0A2W1HKH4_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_G3R1E6_G3R1E6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_H2NSD6_H2NSD6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_F6XRW3_F6XRW3_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_K7BP32_K7BP32_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_I3MJF2_I3MJF2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_H0XBW0_H0XBW0_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and sp_O43896_KIF1C_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_I2CWB9_I2CWB9_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_G5BW92_G5BW92_HETGA_10181 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A091CYD5_A0A091CYD5_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A1U7U5X2_A0A1U7U5X2_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2K5MCT7_A0A2K5MCT7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2K5Z4W9_A0A2K5Z4W9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2R9C1I9_A0A2R9C1I9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2U4AP02_A0A2U4AP02_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2U3ZDV2_A0A2U3ZDV2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2Y9L3B4_A0A2Y9L3B4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1P9P9_G1P9P9_MYOLU_59463 and tr_A0A2Y9SYT8_A0A2Y9SYT8_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_B0CSG5_B0CSG5_LACBS_486041 and tr_A0A0C9X8R8_A0A0C9X8R8_9AGAR_1095629 are exactly identical!
WARNING: Sequences tr_B6Q7D9_B6Q7D9_TALMQ_441960 and tr_B8M662_B8M662_TALSN_441959 are exactly identical!
WARNING: Sequences tr_B6Q7D9_B6Q7D9_TALMQ_441960 and tr_A0A093W160_A0A093W160_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_D8QNF5_D8QNF5_SELML_88036 and tr_D8RDN2_D8RDN2_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_H2N379_H2N379_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_H2R7Y5_H2R7Y5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A1D5QF70_A0A1D5QF70_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A096MRZ2_A0A096MRZ2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A0D9R9V8_A0A0D9R9V8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A2K5NAT4_A0A2K5NAT4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A2K5YQV5_A0A2K5YQV5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3R4E6_G3R4E6_GORGO_9595 and tr_A0A2R9BC10_A0A2R9BC10_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RF78_G3RF78_GORGO_9595 and tr_H2N8Q7_H2N8Q7_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RF78_G3RF78_GORGO_9595 and tr_F7ES46_F7ES46_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RF78_G3RF78_GORGO_9595 and tr_A0A096MZW0_A0A096MZW0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RF78_G3RF78_GORGO_9595 and tr_A0A0D9S8C0_A0A0D9S8C0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RF78_G3RF78_GORGO_9595 and tr_A0A2K6BA34_A0A2K6BA34_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and tr_H2RC47_H2RC47_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and sp_Q9ULI4_KI26A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and tr_F6YUV1_F6YUV1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and tr_A0A2K5MD51_A0A2K5MD51_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and tr_A0A2K6CXD8_A0A2K6CXD8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3S0V0_G3S0V0_GORGO_9595 and tr_A0A2K6A7N6_A0A2K6A7N6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A8BB91_A8BB91_GIAIC_184922 and tr_E1EXY9_E1EXY9_GIAIA_658858 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_G1KMV8_G1KMV8_ANOCA_28377 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_F6YNZ5_F6YNZ5_ORNAN_9258 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_H0XDE4_H0XDE4_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_G5ASQ1_G5ASQ1_HETGA_10181 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_G3T4C1_G3T4C1_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_G3WEX0_G3WEX0_SARHA_9305 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_U3KG94_U3KG94_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_A0A3Q0DT28_A0A3Q0DT28_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_A0A2Y9RJZ0_A0A2Y9RJZ0_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_A0A384C5Y5_A0A384C5Y5_URSMA_29073 are exactly identical!
WARNING: Sequences tr_H2PGI5_H2PGI5_PONAB_9601 and tr_A0A384AMM3_A0A384AMM3_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G1SUQ8_G1SUQ8_RABIT_9986 and tr_J9PAB8_J9PAB8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1SUQ8_G1SUQ8_RABIT_9986 and tr_A0A287CYK3_A0A287CYK3_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1SUQ8_G1SUQ8_RABIT_9986 and tr_A0A1S3AGS1_A0A1S3AGS1_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_Q29MB2_KI26L_DROPS_46245 and tr_B4G9H8_B4G9H8_DROPE_7234 are exactly identical!
WARNING: Sequences tr_F6UVS3_F6UVS3_MONDO_13616 and tr_G3WDP4_G3WDP4_SARHA_9305 are exactly identical!
WARNING: Sequences tr_F7F861_F7F861_MONDO_13616 and tr_G3VZG3_G3VZG3_SARHA_9305 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_H3GZK5_H3GZK5_PHYRM_164328 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_W2Q0C1_W2Q0C1_PHYPN_761204 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_A0A0W8BPJ0_A0A0W8BPJ0_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_A0A0W8DVX0_A0A0W8DVX0_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_W2KWS8_W2KWS8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_G4Z459_G4Z459_PHYSP_1094619 and tr_A0A329S5M8_A0A329S5M8_9STRA_29920 are exactly identical!
WARNING: Sequences tr_A0A3B5QZS1_A0A3B5QZS1_XIPMA_8083 and tr_A0A087YB68_A0A087YB68_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M3ZHX7_M3ZHX7_XIPMA_8083 and tr_A0A087X6N6_A0A087X6N6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A087ZX38_A0A087ZX38_APIME_7460 and tr_A0A2A3EBG7_A0A2A3EBG7_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_E2BGI9_E2BGI9_HARSA_610380 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A026WYI0_A0A026WYI0_OOCBI_2015173 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A0M8ZZ47_A0A0M8ZZ47_9HYME_166423 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A151WG67_A0A151WG67_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A195E6E6_A0A195E6E6_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A195B1I4_A0A195B1I4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A195EYZ2_A0A195EYZ2_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A087ZZ54_A0A087ZZ54_APIME_7460 and tr_A0A151IB55_A0A151IB55_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A088A1K2_A0A088A1K2_APIME_7460 and tr_A0A0M8ZQ99_A0A0M8ZQ99_9HYME_166423 are exactly identical!
WARNING: Sequences tr_A0A088A1K2_A0A088A1K2_APIME_7460 and tr_A0A2A3EHV1_A0A2A3EHV1_APICC_94128 are exactly identical!
WARNING: Sequences tr_I3KN70_I3KN70_ORENI_8128 and tr_A0A087XWT4_A0A087XWT4_POEFO_48698 are exactly identical!
WARNING: Sequences tr_I3KN70_I3KN70_ORENI_8128 and tr_A0A2I4B9P5_A0A2I4B9P5_9TELE_52670 are exactly identical!
WARNING: Sequences tr_H0UVB9_H0UVB9_CAVPO_10141 and tr_A0A091D4M7_A0A091D4M7_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_D0NAK3_D0NAK3_PHYIT_403677 and tr_W2PZR3_W2PZR3_PHYPN_761204 are exactly identical!
WARNING: Sequences tr_D0NAK3_D0NAK3_PHYIT_403677 and tr_A0A0W8DX40_A0A0W8DX40_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_D0NAK3_D0NAK3_PHYIT_403677 and tr_W2KWP2_W2KWP2_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_D0NAK3_D0NAK3_PHYIT_403677 and tr_A0A329T1C7_A0A329T1C7_9STRA_29920 are exactly identical!
WARNING: Sequences tr_A0A0H5S9H6_A0A0H5S9H6_BRUMA_6279 and tr_A0A0R3QY88_A0A0R3QY88_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_G7XM93_G7XM93_ASPKW_1033177 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_G3YG55_G3YG55_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A0L1JED2_A0A0L1JED2_ASPNO_1509407 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A100IPV7_A0A100IPV7_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A146FAM8_A0A146FAM8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A1L9NQF7_A0A1L9NQF7_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A317UWU6_A0A317UWU6_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A319ALY3_A0A319ALY3_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V0SBA4_A0A0V0SBA4_9BILA_6336 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V1CHN2_A0A0V1CHN2_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V0X9T9_A0A0V0X9T9_9BILA_92179 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V1KUC4_A0A0V1KUC4_9BILA_6335 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V1P260_A0A0V1P260_9BILA_92180 are exactly identical!
WARNING: Sequences tr_E5S1E3_E5S1E3_TRISP_6334 and tr_A0A0V0TJ09_A0A0V0TJ09_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A2WSD1_A2WSD1_ORYSI_39946 and tr_A0A0D9YBG4_A0A0D9YBG4_9ORYZ_40148 are exactly identical!
WARNING: Sequences sp_Q9GYZ0_KIF15_STRPU_7668 and tr_W4YZN7_W4YZN7_STRPU_7668 are exactly identical!
WARNING: Sequences tr_K7FCZ3_K7FCZ3_PELSI_13735 and tr_A0A093ILQ8_A0A093ILQ8_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_I1NPG8_I1NPG8_ORYGL_4538 and tr_A0A0D3ER10_A0A0D3ER10_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F4WKD7_F4WKD7_ACREC_103372 and tr_A0A195ERI8_A0A195ERI8_9HYME_34720 are exactly identical!
WARNING: Sequences tr_E6R1C6_E6R1C6_CRYGW_367775 and tr_A0A095DI05_A0A095DI05_CRYGR_294750 are exactly identical!
WARNING: Sequences tr_A0A0E0MZ11_A0A0E0MZ11_ORYRU_4529 and sp_Q0JLE4_KN8A_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9X021_F9X021_ZYMTI_336722 and tr_A0A0F4GJI0_A0A0F4GJI0_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9X021_F9X021_ZYMTI_336722 and tr_A0A1X7RDZ9_A0A1X7RDZ9_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G0MP98_G0MP98_CAEBE_135651 and tr_G0MPA0_G0MPA0_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_F7B3N7_F7B3N7_XENTR_8364 and tr_A0A1L8GXL6_A0A1L8GXL6_XENLA_8355 are exactly identical!
WARNING: Sequences tr_F7DZJ6_F7DZJ6_XENTR_8364 and tr_A0A1L8G2C3_A0A1L8G2C3_XENLA_8355 are exactly identical!
WARNING: Sequences tr_E2B6U2_E2B6U2_HARSA_610380 and tr_A0A151J2C0_A0A151J2C0_9HYME_471704 are exactly identical!
WARNING: Sequences tr_E2B6U2_E2B6U2_HARSA_610380 and tr_A0A195CM39_A0A195CM39_9HYME_456900 are exactly identical!
WARNING: Sequences tr_E3MSP2_E3MSP2_CAERE_31234 and tr_A0A261AU78_A0A261AU78_9PELO_1503980 are exactly identical!
WARNING: Sequences sp_Q60LV7_KI26L_CAEBR_6238 and tr_A0A2G5TH37_A0A2G5TH37_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_G1LRB5_G1LRB5_AILME_9646 and tr_A0A2Y9JTY2_A0A2Y9JTY2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_B3SAV1_B3SAV1_TRIAD_10228 and tr_A0A369S885_A0A369S885_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A287L2E0_A0A287L2E0_HORVV_112509 and tr_A0A077RWX9_A0A077RWX9_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_U3JJV1_U3JJV1_FICAL_59894 and tr_A0A091EIG9_A0A091EIG9_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3JJV1_U3JJV1_FICAL_59894 and tr_A0A218UR71_A0A218UR71_9PASE_299123 are exactly identical!
WARNING: Sequences tr_U3KAK2_U3KAK2_FICAL_59894 and tr_A0A091EB30_A0A091EB30_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3KAK2_U3KAK2_FICAL_59894 and tr_A0A093SU82_A0A093SU82_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3KAK2_U3KAK2_FICAL_59894 and tr_A0A218V329_A0A218V329_9PASE_299123 are exactly identical!
WARNING: Sequences tr_U3KDA6_U3KDA6_FICAL_59894 and tr_A0A091EVW8_A0A091EVW8_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3KDA6_U3KDA6_FICAL_59894 and tr_A0A093S346_A0A093S346_9PASS_328815 are exactly identical!
WARNING: Sequences tr_V2XTA9_V2XTA9_MONRO_1381753 and tr_A0A0W0F996_A0A0W0F996_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QBR8_W2QBR8_PHYPN_761204 and tr_A0A0W8CBF1_A0A0W8CBF1_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QBR8_W2QBR8_PHYPN_761204 and tr_W2LCC9_W2LCC9_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2R7Q8_W2R7Q8_PHYPN_761204 and tr_A0A0W8C439_A0A0W8C439_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2R7Q8_W2R7Q8_PHYPN_761204 and tr_W2KTT8_W2KTT8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W4GWD4_W4GWD4_9STRA_112090 and tr_A0A024U8V4_A0A024U8V4_9STRA_157072 are exactly identical!
WARNING: Sequences tr_A0A3B6EHU4_A0A3B6EHU4_WHEAT_4565 and tr_A0A3B6GWL5_A0A3B6GWL5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067FQ15_A0A067FQ15_CITSI_2711 and tr_V4TW75_V4TW75_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FQ15_A0A067FQ15_CITSI_2711 and tr_A0A2H5Q7C1_A0A2H5Q7C1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A074WGD2_A0A074WGD2_9PEZI_1043004 and tr_A0A074XEL6_A0A074XEL6_AURPU_1043002 are exactly identical!
WARNING: Sequences tr_A0A0A0LPH4_A0A0A0LPH4_CUCSA_3659 and tr_A0A1S3BW14_A0A1S3BW14_CUCME_3656 are exactly identical!
WARNING: Sequences tr_A0A067CMC3_A0A067CMC3_SAPPC_695850 and tr_T0PUW9_T0PUW9_9STRA_1156394 are exactly identical!
WARNING: Sequences tr_A0A0D2NZE6_A0A0D2NZE6_GOSRA_29730 and tr_A0A1U8HKU5_A0A1U8HKU5_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2NZE6_A0A0D2NZE6_GOSRA_29730 and tr_A0A1U8NLU0_A0A1U8NLU0_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0K8LLN2_A0A0K8LLN2_9EURO_91492 and tr_A0A229YZ34_A0A229YZ34_9EURO_1245748 are exactly identical!
WARNING: Sequences tr_A0A0K8LLN2_A0A0K8LLN2_9EURO_91492 and tr_A0A2I1CBA1_A0A2I1CBA1_9EURO_1392255 are exactly identical!
WARNING: Sequences tr_A0A0L6UZK1_A0A0L6UZK1_9BASI_27349 and tr_A0A2N5SX34_A0A2N5SX34_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A151M259_A0A151M259_ALLMI_8496 and tr_A0A1U8CU89_A0A1U8CU89_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151MH60_A0A151MH60_ALLMI_8496 and tr_A0A3Q0GRZ9_A0A3Q0GRZ9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151NNW2_A0A151NNW2_ALLMI_8496 and tr_A0A1U7RSD0_A0A1U7RSD0_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A093PZ78_A0A093PZ78_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A091V876_A0A091V876_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A0A0A8F0_A0A0A0A8F0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A2I0MPQ3_A0A2I0MPQ3_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A091IAG0_A0A091IAG0_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0Q3X7T9_A0A0Q3X7T9_AMAAE_12930 and tr_A0A1V4KAB0_A0A1V4KAB0_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A194RDQ9_A0A194RDQ9_PAPMA_76193 and tr_A0A194PV48_A0A194PV48_PAPXU_66420 are exactly identical!
WARNING: Sequences tr_A0A087QU47_A0A087QU47_APTFO_9233 and tr_A0A099ZAK6_A0A099ZAK6_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A2I0LKH2_A0A2I0LKH2_COLLI_8932 and tr_A0A1V4JGY4_A0A1V4JGY4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MVM5_A0A2I0MVM5_COLLI_8932 and tr_A0A1V4JKT1_A0A1V4JKT1_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1DI03_A0A0V1DI03_TRIBR_45882 and tr_A0A0V0XAG9_A0A0V0XAG9_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DI03_A0A0V1DI03_TRIBR_45882 and tr_A0A0V0VQZ0_A0A0V0VQZ0_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1DI03_A0A0V1DI03_TRIBR_45882 and tr_A0A0V1L999_A0A0V1L999_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1DI03_A0A0V1DI03_TRIBR_45882 and tr_A0A0V1P7K1_A0A0V1P7K1_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1MT27_A0A0V1MT27_9BILA_268474 and tr_A0A0V1H0W5_A0A0V1H0W5_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A0V1MWT5_A0A0V1MWT5_9BILA_268474 and tr_A0A0V1HWS9_A0A0V1HWS9_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A0P1BPM8_A0A0P1BPM8_9BASI_401625 and tr_A0A316W535_A0A316W535_9BASI_1522189 are exactly identical!
WARNING: Sequences tr_A0A1S4BDX3_A0A1S4BDX3_TOBAC_4097 and tr_A0A1U7VQJ6_A0A1U7VQJ6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3H4K2_A0A1S3H4K2_LINUN_7574 and tr_A0A1S3K130_A0A1S3K130_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3LQA1_A0A1S3LQA1_SALSA_8030 and tr_A0A1S3SMX4_A0A1S3SMX4_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1L9PUU4_A0A1L9PUU4_ASPVE_1036611 and tr_A0A1L9T468_A0A1L9T468_9EURO_1036612 are exactly identical!
WARNING: Sequences tr_A0A1L9WPN2_A0A1L9WPN2_ASPAC_690307 and tr_A0A319C296_A0A319C296_9EURO_1448315 are exactly identical!
WARNING: Sequences tr_A0A1L9WPN2_A0A1L9WPN2_ASPAC_690307 and tr_A0A318ZHF0_A0A318ZHF0_9EURO_1450539 are exactly identical!
WARNING: Sequences tr_A0A1L9WPN2_A0A1L9WPN2_ASPAC_690307 and tr_A0A2V5IFK1_A0A2V5IFK1_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A1L9WPN2_A0A1L9WPN2_ASPAC_690307 and tr_A0A395HYB2_A0A395HYB2_9EURO_1450537 are exactly identical!
WARNING: Sequences tr_A0A1L9WPN2_A0A1L9WPN2_ASPAC_690307 and tr_A0A2V5H907_A0A2V5H907_9EURO_1450538 are exactly identical!
WARNING: Sequences tr_A0A1D1VJL1_A0A1D1VJL1_RAMVA_947166 and tr_A0A1D1VQ09_A0A1D1VQ09_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1R3S0X8_A0A1R3S0X8_ASPC5_602072 and tr_A0A317VLT7_A0A317VLT7_9EURO_1450535 are exactly identical!
WARNING: Sequences tr_A0A1R3S0X8_A0A1R3S0X8_ASPC5_602072 and tr_A0A319ENL8_A0A319ENL8_9EURO_1448318 are exactly identical!
WARNING: Sequences tr_A0A1V8U7R6_A0A1V8U7R6_9PEZI_1974281 and tr_A0A1V8T5X8_A0A1V8T5X8_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1V8UDH5_A0A1V8UDH5_9PEZI_1974281 and tr_A0A1V8TNN7_A0A1V8TNN7_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1Z5TA16_A0A1Z5TA16_HORWE_1157616 and tr_A0A1Z5TJX8_A0A1Z5TJX8_HORWE_1157616 are exactly identical!
WARNING: Sequences tr_A0A226MLX6_A0A226MLX6_CALSU_9009 and tr_A0A226P0M9_A0A226P0M9_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2H3CG44_A0A2H3CG44_9AGAR_1076256 and tr_A0A284QVI5_A0A284QVI5_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2D0RPD0_A0A2D0RPD0_ICTPU_7998 and tr_A0A2D0RPD1_A0A2D0RPD1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPD0_A0A2D0RPD0_ICTPU_7998 and tr_A0A2D0RQC0_A0A2D0RQC0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2G5ICE9_A0A2G5ICE9_CERBT_122368 and tr_A0A2S6C8R0_A0A2S6C8R0_9PEZI_357750 are exactly identical!
WARNING: Sequences tr_A0A2N5SR34_A0A2N5SR34_9BASI_200324 and tr_A0A2N5VK99_A0A2N5VK99_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A2U4A574_A0A2U4A574_TURTR_9739 and tr_A0A2Y9TET2_A0A2Y9TET2_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4A574_A0A2U4A574_TURTR_9739 and tr_A0A383YWU3_A0A383YWU3_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 217

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.reduced.phy

Alignment comprises 1 partitions and 205 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 205 / 205
Gaps: 2.13 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.rba

Parallelization scheme autoconfig: 4 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 1000 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 205 / 16400
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -324428.659423] Initial branch length optimization
[00:00:06 -270182.925656] Model parameter optimization (eps = 10.000000)
[00:00:52 -269832.382528] AUTODETECT spr round 1 (radius: 5)
[00:04:03 -163680.008761] AUTODETECT spr round 2 (radius: 10)
[00:07:20 -114774.125216] AUTODETECT spr round 3 (radius: 15)
[00:10:28 -90359.359225] AUTODETECT spr round 4 (radius: 20)
[00:14:02 -76404.771492] AUTODETECT spr round 5 (radius: 25)
[00:18:56 -68765.179870] SPR radius for FAST iterations: 25 (autodetect)
[00:18:56 -68765.179870] Model parameter optimization (eps = 3.000000)
[00:19:25 -68716.777544] FAST spr round 1 (radius: 25)
[00:22:26 -58156.505277] FAST spr round 2 (radius: 25)
[00:24:42 -57765.878914] FAST spr round 3 (radius: 25)
[00:26:45 -57714.214401] FAST spr round 4 (radius: 25)
[00:28:36 -57711.577800] FAST spr round 5 (radius: 25)
[00:30:21 -57711.576680] Model parameter optimization (eps = 1.000000)
[00:30:37 -57709.187793] SLOW spr round 1 (radius: 5)
[00:33:04 -57695.429759] SLOW spr round 2 (radius: 5)
[00:35:24 -57693.629713] SLOW spr round 3 (radius: 5)
[00:37:39 -57693.627941] SLOW spr round 4 (radius: 10)
[00:39:59 -57693.626742] SLOW spr round 5 (radius: 15)
[00:43:54 -57693.625829] SLOW spr round 6 (radius: 20)
[00:49:45 -57693.625134] SLOW spr round 7 (radius: 25)
[00:57:24 -57693.624604] Model parameter optimization (eps = 0.100000)

[00:57:29] [worker #0] ML tree search #1, logLikelihood: -57693.574322

[00:57:30 -325002.496954] Initial branch length optimization
[00:57:36 -269919.729156] Model parameter optimization (eps = 10.000000)
[00:58:14 -269528.438805] AUTODETECT spr round 1 (radius: 5)
[01:01:24 -167740.882436] AUTODETECT spr round 2 (radius: 10)
[01:04:49 -118349.106181] AUTODETECT spr round 3 (radius: 15)
[01:08:22 -91630.232554] AUTODETECT spr round 4 (radius: 20)
[01:12:03 -79304.269018] AUTODETECT spr round 5 (radius: 25)
[01:15:17] [worker #1] ML tree search #2, logLikelihood: -57673.467902
[01:17:11 -72835.662302] SPR radius for FAST iterations: 25 (autodetect)
[01:17:11 -72835.662302] Model parameter optimization (eps = 3.000000)
[01:17:37 -72806.232529] FAST spr round 1 (radius: 25)
[01:20:42 -58853.313853] FAST spr round 2 (radius: 25)
[01:22:57 -57774.751468] FAST spr round 3 (radius: 25)
[01:24:58 -57715.847653] FAST spr round 4 (radius: 25)
[01:26:50 -57710.148011] FAST spr round 5 (radius: 25)
[01:28:36 -57710.147326] Model parameter optimization (eps = 1.000000)
[01:28:56 -57695.814117] SLOW spr round 1 (radius: 5)
[01:31:18 -57675.445376] SLOW spr round 2 (radius: 5)
[01:32:57] [worker #2] ML tree search #3, logLikelihood: -57697.260559
[01:33:40 -57674.893907] SLOW spr round 3 (radius: 5)
[01:35:54 -57674.893581] SLOW spr round 4 (radius: 10)
[01:38:16 -57673.096412] SLOW spr round 5 (radius: 5)
[01:41:13 -57673.096276] SLOW spr round 6 (radius: 10)
[01:43:52 -57673.096182] SLOW spr round 7 (radius: 15)
[01:47:34 -57671.598297] SLOW spr round 8 (radius: 5)
[01:49:30] [worker #3] ML tree search #4, logLikelihood: -57662.708830
[01:50:40 -57671.504549] SLOW spr round 9 (radius: 10)
[01:53:27 -57671.504023] SLOW spr round 10 (radius: 15)
[01:57:11 -57671.503996] SLOW spr round 11 (radius: 20)
[02:03:46 -57671.503985] SLOW spr round 12 (radius: 25)
[02:12:04 -57671.503978] Model parameter optimization (eps = 0.100000)

[02:12:17] [worker #0] ML tree search #5, logLikelihood: -57670.804252

[02:12:17 -321261.739650] Initial branch length optimization
[02:12:23 -265252.836037] Model parameter optimization (eps = 10.000000)
[02:13:06 -264938.936939] AUTODETECT spr round 1 (radius: 5)
[02:16:13 -165919.104499] AUTODETECT spr round 2 (radius: 10)
[02:19:32 -118076.473557] AUTODETECT spr round 3 (radius: 15)
[02:23:13 -89710.471627] AUTODETECT spr round 4 (radius: 20)
[02:27:17 -74761.701444] AUTODETECT spr round 5 (radius: 25)
[02:31:34 -71477.731441] SPR radius for FAST iterations: 25 (autodetect)
[02:31:34 -71477.731441] Model parameter optimization (eps = 3.000000)
[02:32:00 -71443.181842] FAST spr round 1 (radius: 25)
[02:34:55 -58941.161383] FAST spr round 2 (radius: 25)
[02:37:07 -58221.514020] FAST spr round 3 (radius: 25)
[02:39:09 -57735.727314] FAST spr round 4 (radius: 25)
[02:41:04 -57710.625930] FAST spr round 5 (radius: 25)
[02:42:49 -57710.624499] Model parameter optimization (eps = 1.000000)
[02:43:05 -57706.090550] SLOW spr round 1 (radius: 5)
[02:43:16] [worker #1] ML tree search #6, logLikelihood: -57681.381997
[02:45:04] [worker #2] ML tree search #7, logLikelihood: -57684.965495
[02:45:28 -57689.206019] SLOW spr round 2 (radius: 5)
[02:47:51 -57686.062674] SLOW spr round 3 (radius: 5)
[02:50:09 -57685.352516] SLOW spr round 4 (radius: 5)
[02:52:24 -57685.352360] SLOW spr round 5 (radius: 10)
[02:54:47 -57684.612400] SLOW spr round 6 (radius: 5)
[02:55:44] [worker #3] ML tree search #8, logLikelihood: -57675.120134
[02:57:44 -57684.612235] SLOW spr round 7 (radius: 10)
[03:00:25 -57684.612168] SLOW spr round 8 (radius: 15)
[03:04:01 -57680.472085] SLOW spr round 9 (radius: 5)
[03:07:09 -57680.469726] SLOW spr round 10 (radius: 10)
[03:09:57 -57680.468763] SLOW spr round 11 (radius: 15)
[03:13:33 -57679.085686] SLOW spr round 12 (radius: 5)
[03:16:42 -57678.242534] SLOW spr round 13 (radius: 5)
[03:19:24 -57678.242525] SLOW spr round 14 (radius: 10)
[03:21:56 -57678.242521] SLOW spr round 15 (radius: 15)
[03:25:36 -57678.242519] SLOW spr round 16 (radius: 20)
[03:31:29 -57678.242518] SLOW spr round 17 (radius: 25)
[03:39:06 -57677.658617] SLOW spr round 18 (radius: 5)
[03:41:57] [worker #2] ML tree search #11, logLikelihood: -57676.345520
[03:42:18 -57677.658597] SLOW spr round 19 (radius: 10)
[03:45:10 -57677.658594] SLOW spr round 20 (radius: 15)
[03:48:43 -57677.658593] SLOW spr round 21 (radius: 20)
[03:53:45] [worker #1] ML tree search #10, logLikelihood: -57682.393423
[03:54:40 -57677.658593] SLOW spr round 22 (radius: 25)
[04:02:16 -57677.658593] Model parameter optimization (eps = 0.100000)

[04:02:29] [worker #0] ML tree search #9, logLikelihood: -57677.234445

[04:02:29 -322772.325955] Initial branch length optimization
[04:02:35 -268811.785381] Model parameter optimization (eps = 10.000000)
[04:03:22 -268415.318555] AUTODETECT spr round 1 (radius: 5)
[04:06:31 -169154.528911] AUTODETECT spr round 2 (radius: 10)
[04:09:51 -120029.035757] AUTODETECT spr round 3 (radius: 15)
[04:11:50] [worker #3] ML tree search #12, logLikelihood: -57669.698744
[04:13:17 -100916.523794] AUTODETECT spr round 4 (radius: 20)
[04:17:16 -87335.022014] AUTODETECT spr round 5 (radius: 25)
[04:22:25 -76497.115218] SPR radius for FAST iterations: 25 (autodetect)
[04:22:25 -76497.115218] Model parameter optimization (eps = 3.000000)
[04:22:49 -76459.949157] FAST spr round 1 (radius: 25)
[04:25:53 -59768.697593] FAST spr round 2 (radius: 25)
[04:28:10 -57843.750195] FAST spr round 3 (radius: 25)
[04:30:11 -57741.771852] FAST spr round 4 (radius: 25)
[04:32:04 -57735.904647] FAST spr round 5 (radius: 25)
[04:33:51 -57734.279828] FAST spr round 6 (radius: 25)
[04:35:35 -57734.278924] Model parameter optimization (eps = 1.000000)
[04:35:53 -57705.318985] SLOW spr round 1 (radius: 5)
[04:38:16 -57690.268977] SLOW spr round 2 (radius: 5)
[04:40:32 -57688.403515] SLOW spr round 3 (radius: 5)
[04:42:47 -57688.402900] SLOW spr round 4 (radius: 10)
[04:45:13 -57676.820854] SLOW spr round 5 (radius: 5)
[04:48:15 -57676.528873] SLOW spr round 6 (radius: 5)
[04:50:50 -57676.528863] SLOW spr round 7 (radius: 10)
[04:52:55] [worker #2] ML tree search #15, logLikelihood: -57680.120818
[04:53:18 -57676.528862] SLOW spr round 8 (radius: 15)
[04:57:07 -57676.528862] SLOW spr round 9 (radius: 20)
[05:03:29 -57676.528862] SLOW spr round 10 (radius: 25)
[05:11:59 -57676.528862] Model parameter optimization (eps = 0.100000)

[05:12:07] [worker #0] ML tree search #13, logLikelihood: -57676.388915

[05:12:07 -323321.243567] Initial branch length optimization
[05:12:12 -269529.802150] Model parameter optimization (eps = 10.000000)
[05:13:06 -269176.630718] AUTODETECT spr round 1 (radius: 5)
[05:16:16 -164155.350529] AUTODETECT spr round 2 (radius: 10)
[05:19:44 -116588.811698] AUTODETECT spr round 3 (radius: 15)
[05:23:04 -96194.004547] AUTODETECT spr round 4 (radius: 20)
[05:23:08] [worker #1] ML tree search #14, logLikelihood: -57682.260482
[05:27:06 -78696.682059] AUTODETECT spr round 5 (radius: 25)
[05:28:55] [worker #3] ML tree search #16, logLikelihood: -57676.657706
[05:31:34 -72777.425309] SPR radius for FAST iterations: 25 (autodetect)
[05:31:34 -72777.425309] Model parameter optimization (eps = 3.000000)
[05:32:00 -72743.918380] FAST spr round 1 (radius: 25)
[05:35:06 -58910.308042] FAST spr round 2 (radius: 25)
[05:37:28 -58207.757985] FAST spr round 3 (radius: 25)
[05:39:33 -57715.916679] FAST spr round 4 (radius: 25)
[05:41:29 -57710.634032] FAST spr round 5 (radius: 25)
[05:43:15 -57710.632453] Model parameter optimization (eps = 1.000000)
[05:43:33 -57701.102926] SLOW spr round 1 (radius: 5)
[05:45:58 -57690.928055] SLOW spr round 2 (radius: 5)
[05:48:21 -57689.252778] SLOW spr round 3 (radius: 5)
[05:50:37 -57689.250258] SLOW spr round 4 (radius: 10)
[05:52:58 -57688.645750] SLOW spr round 5 (radius: 5)
[05:55:46] [worker #2] ML tree search #19, logLikelihood: -57675.934097
[05:55:54 -57688.645732] SLOW spr round 6 (radius: 10)
[05:58:33 -57688.645730] SLOW spr round 7 (radius: 15)
[06:02:05 -57688.306122] SLOW spr round 8 (radius: 5)
[06:05:12 -57688.306110] SLOW spr round 9 (radius: 10)
[06:07:57 -57688.306109] SLOW spr round 10 (radius: 15)
[06:11:27 -57688.306109] SLOW spr round 11 (radius: 20)
[06:17:16 -57687.796157] SLOW spr round 12 (radius: 5)
[06:20:26 -57687.782932] SLOW spr round 13 (radius: 10)
[06:23:16 -57687.782745] SLOW spr round 14 (radius: 15)
[06:24:19] [worker #1] ML tree search #18, logLikelihood: -57682.138656
[06:26:32] [worker #3] ML tree search #20, logLikelihood: -57683.872490
[06:26:42 -57687.782735] SLOW spr round 15 (radius: 20)
[06:32:20 -57687.782735] SLOW spr round 16 (radius: 25)
[06:39:39 -57687.782735] Model parameter optimization (eps = 0.100000)

[06:39:53] [worker #0] ML tree search #17, logLikelihood: -57687.281857


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.340026,0.443554) (0.355342,0.624500) (0.197080,1.474394) (0.107552,3.130542) 
   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: -57662.708830

AIC score: 119331.417661 / AICc score: 8147355.417661 / BIC score: 125987.406649
Free parameters (model + branch lengths): 2003

WARNING: Number of free parameters (K=2003) is larger than alignment size (n=205).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 286 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULI4/3_mltree/Q9ULI4.raxml.log

Analysis started: 04-Jul-2021 15:31:42 / finished: 04-Jul-2021 22:11:35

Elapsed time: 23993.652 seconds