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 04-Jul-2021 19:39:43 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/2_msa/Q96PU5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5 --seed 2 --threads 6 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/2_msa/Q96PU5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 389 sites WARNING: Sequences tr_B4QNW6_B4QNW6_DROSI_7240 and sp_Q9VVI3_NEDD4_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5PQP3_A0A1D5PQP3_CHICK_9031 and tr_G1MTE4_G1MTE4_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PZL4_A0A1D5PZL4_CHICK_9031 and tr_U3IN77_U3IN77_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PZL4_A0A1D5PZL4_CHICK_9031 and tr_A0A091GV38_A0A091GV38_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PZL4_A0A1D5PZL4_CHICK_9031 and tr_A0A226MZJ5_A0A226MZJ5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PZL4_A0A1D5PZL4_CHICK_9031 and tr_A0A226PC55_A0A226PC55_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1BWY8_E1BWY8_CHICK_9031 and tr_G1N2I2_G1N2I2_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_H0ZND1_H0ZND1_TAEGU_59729 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_U3JR06_U3JR06_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_U3I3R0_U3I3R0_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A0Q3UQY6_A0A0Q3UQY6_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091EGY8_A0A091EGY8_CORBR_85066 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091J0I7_A0A091J0I7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A093QB68_A0A093QB68_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091UQD9_A0A091UQD9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A087QVU0_A0A087QVU0_APTFO_9233 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091VNX4_A0A091VNX4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091FYA1_A0A091FYA1_9AVES_55661 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A0A0AW30_A0A0A0AW30_CHAVO_50402 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A2I0MXW4_A0A2I0MXW4_COLLI_8932 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A093G819_A0A093G819_DRYPU_118200 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A091HQ52_A0A091HQ52_CALAN_9244 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A1V4KIF5_A0A1V4KIF5_PATFA_372326 are exactly identical! WARNING: Sequences tr_Q5F372_Q5F372_CHICK_9031 and tr_A0A218V5Z2_A0A218V5Z2_9PASE_299123 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_G1QM19_G1QM19_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_E2RSE2_E2RSE2_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_W5PSS2_W5PSS2_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_Q4V8H7_Q4V8H7_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_H0X671_H0X671_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_F7GXT3_F7GXT3_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_F1RXD3_F1RXD3_PIG_9823 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_Q32PG0_Q32PG0_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_M3WRR6_M3WRR6_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A096MQS5_A0A096MQS5_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A091CVL9_A0A091CVL9_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A0D9RKR6_A0A0D9RKR6_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A1S3W469_A0A1S3W469_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A2K5LPS3_A0A2K5LPS3_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A2U3VGR6_A0A2U3VGR6_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A2Y9J9X6_A0A2Y9J9X6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A384BYM6_A0A384BYM6_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q8BZZ3_WWP1_MOUSE_10090 and tr_A0A383ZM40_A0A383ZM40_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_M3YYG0_M3YYG0_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2I2YD63_A0A2I2YD63_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_H2NWF4_H2NWF4_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_G1T7I0_G1T7I0_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2I3REX5_A0A2I3REX5_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_F6WJX8_F6WJX8_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_W5P5V1_W5P5V1_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A0G2JXP3_A0A0G2JXP3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_I3MJW6_I3MJW6_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_H0XDN9_H0XDN9_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and sp_Q96PU5_NED4L_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A1D5RJX1_A0A1D5RJX1_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_G5AYX9_G5AYX9_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_G3T6W8_G3T6W8_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2R8PLC7_A0A2R8PLC7_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_G1M9J3_G1M9J3_AILME_9646 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_G7PWV0_G7PWV0_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_F1MJ09_F1MJ09_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_L5KJY1_L5KJY1_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2I2V4D5_A0A2I2V4D5_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2I3MS57_A0A2I3MS57_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A091D8V2_A0A091D8V2_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A1S3A451_A0A1S3A451_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A1S3FCU4_A0A1S3FCU4_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A3Q0EC00_A0A3Q0EC00_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A3Q0CY13_A0A3Q0CY13_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2K6CED3_A0A2K6CED3_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2K6AB02_A0A2K6AB02_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2R8ZXX8_A0A2R8ZXX8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2U4BHI9_A0A2U4BHI9_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2U3ZQ84_A0A2U3ZQ84_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2U3XTW3_A0A2U3XTW3_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2Y9R5I3_A0A2Y9R5I3_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2Y9K751_A0A2Y9K751_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2Y9P1K5_A0A2Y9P1K5_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A2Y9TCS3_A0A2Y9TCS3_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8CFI0_NED4L_MOUSE_10090 and tr_A0A384D9L0_A0A384D9L0_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XSY4_M3XSY4_MUSPF_9669 and tr_G1MJ76_G1MJ76_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XSY4_M3XSY4_MUSPF_9669 and tr_M3W9A7_M3W9A7_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XSY4_M3XSY4_MUSPF_9669 and tr_A0A2Y9K8H4_A0A2Y9K8H4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_G1T9A1_G1T9A1_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_F7GXU1_F7GXU1_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A286ZL14_A0A286ZL14_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_F1MGQ5_F1MGQ5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A1S3WAL8_A0A1S3WAL8_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A1S3EP31_A0A1S3EP31_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A1U7UIY7_A0A1U7UIY7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A2Y9PYB3_A0A2Y9PYB3_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A2Y9T0Z2_A0A2Y9T0Z2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Z293_M3Z293_MUSPF_9669 and tr_A0A384B201_A0A384B201_BALAS_310752 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_A0A0A2KM38_A0A0A2KM38_PENIT_40296 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_W6Q780_W6Q780_PENRF_1365484 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_A0A0G4P0J5_A0A0G4P0J5_PENCA_1429867 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_A0A101MSW9_A0A101MSW9_9EURO_48697 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_A0A1V6NEE6_A0A1V6NEE6_9EURO_60169 are exactly identical! WARNING: Sequences tr_B6H7J0_B6H7J0_PENRW_500485 and tr_A0A1V6R4V4_A0A1V6R4V4_9EURO_60172 are exactly identical! WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_B2W179_B2W179_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_A0A2W1DRQ7_A0A2W1DRQ7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2I2YF24_A0A2I2YF24_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2I3T8C4_A0A2I3T8C4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and sp_P46934_NEDD4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_F7HIS9_F7HIS9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_G8F512_G8F512_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2I3MEL4_A0A2I3MEL4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A0D9RHB5_A0A0D9RHB5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2K5NMR8_A0A2K5NMR8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2K6C3D9_A0A2K6C3D9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2K5YPT2_A0A2K5YPT2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R4H4_G1R4H4_NOMLE_61853 and tr_A0A2R9BME0_A0A2R9BME0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3HAN9_G3HAN9_CRIGR_10029 and tr_A0A3Q0DE74_A0A3Q0DE74_MESAU_10036 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_E9CRR5_E9CRR5_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_A0A0J6YB63_A0A0J6YB63_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q6Z7_B6Q6Z7_TALMQ_441960 and tr_A0A093VWC5_A0A093VWC5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QWC8_G3QWC8_GORGO_9595 and tr_K7BGN1_K7BGN1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QWC8_G3QWC8_GORGO_9595 and sp_Q96J02_ITCH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RG92_G3RG92_GORGO_9595 and tr_H2QWD9_H2QWD9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RG92_G3RG92_GORGO_9595 and sp_Q9H0M0_WWP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RG92_G3RG92_GORGO_9595 and tr_A0A2R9BAH3_A0A2R9BAH3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2WR90_G2WR90_VERDV_498257 and tr_C9S618_C9S618_VERA1_526221 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_C6H2E0_C6H2E0_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_F0U541_F0U541_AJEC8_544711 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_A6RB21_A6RB21_AJECN_339724 are exactly identical! WARNING: Sequences tr_G1NGU6_G1NGU6_MELGA_9103 and tr_A0A226NNG2_A0A226NNG2_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1NGU6_G1NGU6_MELGA_9103 and tr_A0A226P725_A0A226P725_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q7RV01_Q7RV01_NEUCR_367110 and tr_G4UYR6_G4UYR6_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A0R3P5N2_A0A0R3P5N2_DROPS_46245 and tr_B4HBV9_B4HBV9_DROPE_7234 are exactly identical! WARNING: Sequences sp_B8N7E5_RSP5_ASPFN_332952 and sp_Q2UBP1_RSP5_ASPOR_510516 are exactly identical! WARNING: Sequences sp_B8N7E5_RSP5_ASPFN_332952 and tr_A0A0F0IF99_A0A0F0IF99_ASPPU_1403190 are exactly identical! WARNING: Sequences sp_B8N7E5_RSP5_ASPFN_332952 and tr_A0A1S9DR89_A0A1S9DR89_ASPOZ_5062 are exactly identical! WARNING: Sequences sp_B8N7E5_RSP5_ASPFN_332952 and tr_A0A2G7FRM5_A0A2G7FRM5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_C5GFJ5_C5GFJ5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_A0A1J9PUN1_A0A1J9PUN1_9EURO_1658174 are exactly identical! WARNING: Sequences sp_P39940_RSP5_YEAST_559292 and tr_J6EDQ6_J6EDQ6_SACK1_226230 are exactly identical! WARNING: Sequences tr_W5Q0X0_W5Q0X0_SHEEP_9940 and tr_F1N3W8_F1N3W8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QI99_W5QI99_SHEEP_9940 and tr_F1MJ10_F1MJ10_BOVIN_9913 are exactly identical! WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0B4HP08_A0A0B4HP08_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0D9NSU6_A0A0D9NSU6_METAN_1291518 are exactly identical! WARNING: Sequences sp_Q4WTF3_RSP5_ASPFU_330879 and sp_A1D3C5_RSP5_NEOFI_331117 are exactly identical! WARNING: Sequences sp_Q4WTF3_RSP5_ASPFU_330879 and tr_A0A2I1C9V2_A0A2I1C9V2_9EURO_1392255 are exactly identical! WARNING: Sequences tr_J4USV8_J4USV8_BEAB2_655819 and tr_A0A0A2V9D4_A0A0A2V9D4_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4USV8_J4USV8_BEAB2_655819 and tr_A0A2N6P080_A0A2N6P080_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A3B5R1R8_A0A3B5R1R8_XIPMA_8083 and tr_A0A096LYY4_A0A096LYY4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088A2N6_A0A088A2N6_APIME_7460 and tr_A0A2A3E719_A0A2A3E719_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A286XGM8_A0A286XGM8_CAVPO_10141 and tr_A0A287AX02_A0A287AX02_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A286XGM8_A0A286XGM8_CAVPO_10141 and tr_A0A0D9RZY5_A0A0D9RZY5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A286XGM8_A0A286XGM8_CAVPO_10141 and tr_A0A384AXA1_A0A384AXA1_BALAS_310752 are exactly identical! WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_G3YFP8_G3YFP8_ASPNA_380704 are exactly identical! WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_A0A1L9UQX8_A0A1L9UQX8_9EURO_767769 are exactly identical! WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_A0A319A8D3_A0A319A8D3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_G7PGK1_G7PGK1_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A096NUS9_A0A096NUS9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A0D9RI42_A0A0D9RI42_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5KTB2_A0A2K5KTB2_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K6BGS2_A0A2K6BGS2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5Z4A3_A0A2K5Z4A3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7XKL8_G7XKL8_ASPKW_1033177 and tr_A0A1L9NN16_A0A1L9NN16_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XKL8_G7XKL8_ASPKW_1033177 and tr_A0A317UZC2_A0A317UZC2_9EURO_1448314 are exactly identical! WARNING: Sequences tr_H1VJJ9_H1VJJ9_COLHI_759273 and tr_A0A010S8F5_A0A010S8F5_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_H1VJJ9_H1VJJ9_COLHI_759273 and tr_A0A135SHN6_A0A135SHN6_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_H1VJJ9_H1VJJ9_COLHI_759273 and tr_A0A1G4B1V9_A0A1G4B1V9_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_F4PCI9_F4PCI9_BATDJ_684364 and tr_A0A177WXG0_A0A177WXG0_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0Z7N9_H0Z7N9_TAEGU_59729 and tr_A0A091E5J5_A0A091E5J5_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z7N9_H0Z7N9_TAEGU_59729 and tr_A0A218V8G0_A0A218V8G0_9PASE_299123 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A0Q3LTI5_A0A0Q3LTI5_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A091FME6_A0A091FME6_CORBR_85066 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A091JT42_A0A091JT42_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A091UWN7_A0A091UWN7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A093HBP9_A0A093HBP9_STRCA_441894 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A091W4X5_A0A091W4X5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A0A0A8H6_A0A0A0A8H6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A1V4JGQ5_A0A1V4JGQ5_PATFA_372326 are exactly identical! WARNING: Sequences tr_H1A4F6_H1A4F6_TAEGU_59729 and tr_A0A218UBQ9_A0A218UBQ9_9PASE_299123 are exactly identical! WARNING: Sequences tr_F9XPD8_F9XPD8_ZYMTI_336722 and tr_A0A1X7S762_A0A1X7S762_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YHG2_G2YHG2_BOTF4_999810 and tr_M7UZ78_M7UZ78_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A8Y1X0_A8Y1X0_CAEBR_6238 and tr_A0A2G5VUP0_A0A2G5VUP0_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SLC2_F2SLC2_TRIRC_559305 and tr_D4AUV9_D4AUV9_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SLC2_F2SLC2_TRIRC_559305 and tr_A0A059J980_A0A059J980_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SLC2_F2SLC2_TRIRC_559305 and tr_A0A178EQS6_A0A178EQS6_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G1LRF3_G1LRF3_AILME_9646 and tr_M3WA81_M3WA81_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1LRF3_G1LRF3_AILME_9646 and tr_A0A2U3ZN66_A0A2U3ZN66_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LRF3_G1LRF3_AILME_9646 and tr_A0A2Y9ILU8_A0A2Y9ILU8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1LRF3_G1LRF3_AILME_9646 and tr_A0A384CNI5_A0A384CNI5_URSMA_29073 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A0D2XML3_A0A0D2XML3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_S0E188_S0E188_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_N4U0R5_N4U0R5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_X0C902_X0C902_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3SP11_A0A2H3SP11_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3HCZ8_A0A2H3HCZ8_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2K0WET4_A0A2K0WET4_GIBNY_42673 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A365NL61_A0A365NL61_GIBIN_948311 are exactly identical! WARNING: Sequences tr_K9GCR4_K9GCR4_PEND2_1170229 and tr_A0A135LRH2_A0A135LRH2_PENPA_5078 are exactly identical! WARNING: Sequences tr_K9GCR4_K9GCR4_PEND2_1170229 and tr_A0A1V6RY60_A0A1V6RY60_9EURO_29845 are exactly identical! WARNING: Sequences tr_L8G0S8_L8G0S8_PSED2_658429 and tr_A0A094DKG9_A0A094DKG9_9PEZI_1420910 are exactly identical! WARNING: Sequences tr_L8G0S8_L8G0S8_PSED2_658429 and tr_A0A1B8DXT8_A0A1B8DXT8_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_L8G0S8_L8G0S8_PSED2_658429 and tr_A0A1B8C7K7_A0A1B8C7K7_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_U3KDH3_U3KDH3_FICAL_59894 and tr_A0A093PHC6_A0A093PHC6_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3KDH3_U3KDH3_FICAL_59894 and tr_A0A218UAS3_A0A218UAS3_9PASE_299123 are exactly identical! WARNING: Sequences tr_M2Z2Z1_M2Z2Z1_PSEFD_383855 and tr_A0A139HWE0_A0A139HWE0_9PEZI_321146 are exactly identical! WARNING: Sequences tr_M2SSJ2_M2SSJ2_COCSN_665912 and tr_R0J6H1_R0J6H1_SETT2_671987 are exactly identical! WARNING: Sequences tr_M2SSJ2_M2SSJ2_COCSN_665912 and tr_M2TJR9_M2TJR9_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SSJ2_M2SSJ2_COCSN_665912 and tr_W6Y406_W6Y406_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2SSJ2_M2SSJ2_COCSN_665912 and tr_W6ZAK5_W6ZAK5_COCMI_930090 are exactly identical! WARNING: Sequences tr_W9WJC3_W9WJC3_9EURO_1182544 and tr_A0A1C1CSV9_A0A1C1CSV9_9EURO_86049 are exactly identical! WARNING: Sequences tr_W9Y5P5_W9Y5P5_9EURO_1182542 and tr_W9YUQ4_W9YUQ4_9EURO_1182541 are exactly identical! WARNING: Sequences tr_A0A015LXQ7_A0A015LXQ7_9GLOM_1432141 and tr_A0A2I1FVZ7_A0A2I1FVZ7_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A044QV04_A0A044QV04_ONCVO_6282 and tr_A0A182E0J1_A0A182E0J1_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A094EJM6_A0A094EJM6_9PEZI_1420912 and tr_A0A1B8GLH3_A0A1B8GLH3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F9ZF33_A0A0F9ZF33_TRIHA_5544 and tr_A0A2T4ARA3_A0A2T4ARA3_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8V620_A0A0F8V620_9EURO_308745 and tr_A0A2T5M1N3_A0A2T5M1N3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A2A9PF85_A0A2A9PF85_9HYPO_268505 and tr_A0A2C5ZET2_A0A2C5ZET2_9HYPO_2004952 are exactly identical! WARNING: Sequences tr_A0A0M9EU20_A0A0M9EU20_FUSLA_179993 and tr_I1S0N8_I1S0N8_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0M9EU20_A0A0M9EU20_FUSLA_179993 and tr_A0A1B8B963_A0A1B8B963_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0M9EU20_A0A0M9EU20_FUSLA_179993 and tr_A0A2T4GIH5_A0A2T4GIH5_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0M9EU20_A0A0M9EU20_FUSLA_179993 and tr_A0A2L2TNC9_A0A2L2TNC9_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A0A1NP91_A0A0A1NP91_9FUNG_58291 and tr_A0A0A1NYA7_A0A0A1NYA7_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0A1NP91_A0A0A1NP91_9FUNG_58291 and tr_A0A2G4SYX7_A0A2G4SYX7_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1NP91_A0A0A1NP91_9FUNG_58291 and tr_A0A367JN44_A0A367JN44_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1PJE6_A0A0A1PJE6_9FUNG_58291 and tr_A0A0A1PLP1_A0A0A1PLP1_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0A1PJE6_A0A0A1PJE6_9FUNG_58291 and tr_A0A2G4ST73_A0A2G4ST73_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0F7TXM2_A0A0F7TXM2_9EURO_104259 and tr_A0A1Q5TM73_A0A1Q5TM73_9EURO_1316194 are exactly identical! WARNING: Sequences tr_A0A151M9R4_A0A151M9R4_ALLMI_8496 and tr_A0A3Q0G429_A0A3Q0G429_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P019_A0A151P019_ALLMI_8496 and tr_A0A1U8DXT3_A0A1U8DXT3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0D2A032_A0A0D2A032_9EURO_91928 and tr_A0A0D2B3N9_A0A0D2B3N9_9EURO_215243 are exactly identical! WARNING: Sequences tr_A0A2I0M714_A0A2I0M714_COLLI_8932 and tr_A0A1V4JDH5_A0A1V4JDH5_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0L0RZ82_A0A0L0RZ82_ALLMA_578462 and tr_A0A0L0S7E5_A0A0L0S7E5_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A0V0WUM8_A0A0V0WUM8_9BILA_92179 and tr_A0A0V0VB58_A0A0V0VB58_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1L7S5_A0A0V1L7S5_9BILA_6335 and tr_A0A0V0U1T5_A0A0V0U1T5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A166XU71_A0A166XU71_9PEZI_708197 and tr_A0A161VL31_A0A161VL31_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A177DEL5_A0A177DEL5_ALTAL_5599 and tr_A0A364NCH2_A0A364NCH2_9PLEO_183478 are exactly identical! WARNING: Sequences tr_A0A179G2J7_A0A179G2J7_METCM_1380566 and tr_A0A166YR25_A0A166YR25_9HYPO_1081105 are exactly identical! WARNING: Sequences tr_A0A194WD10_A0A194WD10_9PEZI_105487 and tr_A0A194V3Y5_A0A194V3Y5_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1B7NTF1_A0A1B7NTF1_9EURO_1658172 and tr_A0A1J9PVP1_A0A1J9PVP1_9EURO_1447872 are exactly identical! WARNING: Sequences tr_A0A1B7N8Y7_A0A1B7N8Y7_9HOMO_1314800 and tr_A0A1J8PMS3_A0A1J8PMS3_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1F5L3E7_A0A1F5L3E7_9EURO_1835702 and tr_A0A1V6Q654_A0A1V6Q654_9EURO_416450 are exactly identical! WARNING: Sequences tr_A0A1R3S377_A0A1R3S377_ASPC5_602072 and tr_A0A317WE34_A0A317WE34_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A1V8UBZ0_A0A1V8UBZ0_9PEZI_1974281 and tr_A0A1V8SVT2_A0A1V8SVT2_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1V8UBZ0_A0A1V8UBZ0_9PEZI_1974281 and tr_A0A1V8T1U8_A0A1V8T1U8_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A2H3C4G0_A0A2H3C4G0_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A284QUR2_A0A284QUR2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3BZE7_A0A2H3BZE7_9AGAR_1076256 and tr_A0A284RFW1_A0A284RFW1_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2G5HJG5_A0A2G5HJG5_CERBT_122368 and tr_A0A2S6BRN1_A0A2S6BRN1_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2S7NZY5_A0A2S7NZY5_9HELO_2070414 and tr_A0A2S7PZ27_A0A2S7PZ27_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A319CCM8_A0A319CCM8_9EURO_1448315 and tr_A0A318ZDD6_A0A318ZDD6_9EURO_1450539 are exactly identical! WARNING: Sequences tr_A0A319CCM8_A0A319CCM8_9EURO_1448315 and tr_A0A2V5IP97_A0A2V5IP97_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319CCM8_A0A319CCM8_9EURO_1448315 and tr_A0A2V5HR10_A0A2V5HR10_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A319DWT4_A0A319DWT4_9EURO_1448318 and tr_A0A395GYZ8_A0A395GYZ8_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A369GW94_A0A369GW94_9HYPO_2039875 and tr_A0A369HKP5_A0A369HKP5_9HYPO_2039874 are exactly identical! WARNING: Sequences tr_A0A367XN26_A0A367XN26_9ASCO_5486 and tr_A0A367YNC7_A0A367YNC7_9ASCO_5486 are exactly identical! WARNING: Duplicate sequences found: 250 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/Q96PU5/3_mltree/Q96PU5.raxml.reduced.phy Alignment comprises 1 partitions and 388 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 389 / 388 Gaps: 0.46 % Invariant sites: 5.14 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 194 / 15520 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -408002.447259] Initial branch length optimization [00:00:04 -335970.640245] Model parameter optimization (eps = 10.000000) [00:00:43 -334084.979746] AUTODETECT spr round 1 (radius: 5) [00:03:04 -181927.724684] AUTODETECT spr round 2 (radius: 10) [00:05:23 -109718.850910] AUTODETECT spr round 3 (radius: 15) [00:07:46 -83350.582024] AUTODETECT spr round 4 (radius: 20) [00:10:23 -70129.577687] AUTODETECT spr round 5 (radius: 25) [00:13:33 -68756.246004] SPR radius for FAST iterations: 25 (autodetect) [00:13:33 -68756.246004] Model parameter optimization (eps = 3.000000) [00:13:50 -68719.790981] FAST spr round 1 (radius: 25) [00:15:52 -58570.971008] FAST spr round 2 (radius: 25) [00:17:40 -57494.297668] FAST spr round 3 (radius: 25) [00:19:13 -57314.017203] FAST spr round 4 (radius: 25) [00:20:39 -57259.671056] FAST spr round 5 (radius: 25) [00:22:00 -57255.281897] FAST spr round 6 (radius: 25) [00:23:17 -57255.281354] Model parameter optimization (eps = 1.000000) [00:23:29 -57253.618406] SLOW spr round 1 (radius: 5) [00:25:13 -57248.124038] SLOW spr round 2 (radius: 5) [00:26:53 -57248.001199] SLOW spr round 3 (radius: 5) [00:28:33 -57248.001189] SLOW spr round 4 (radius: 10) [00:30:25 -57228.385748] SLOW spr round 5 (radius: 5) [00:32:41 -57227.864469] SLOW spr round 6 (radius: 5) [00:34:34 -57227.737499] SLOW spr round 7 (radius: 5) [00:36:16 -57227.737497] SLOW spr round 8 (radius: 10) [00:37:59 -57227.737497] SLOW spr round 9 (radius: 15) [00:40:40 -57227.737497] SLOW spr round 10 (radius: 20) [00:42:28] [worker #1] ML tree search #2, logLikelihood: -57246.124115 [00:44:20 -57227.737497] SLOW spr round 11 (radius: 25) [00:45:56] [worker #2] ML tree search #3, logLikelihood: -57274.563410 [00:49:04 -57227.737497] Model parameter optimization (eps = 0.100000) [00:49:08] [worker #0] ML tree search #1, logLikelihood: -57227.696492 [00:49:09 -411999.502019] Initial branch length optimization [00:49:12 -338641.666494] Model parameter optimization (eps = 10.000000) [00:49:49 -336719.766723] AUTODETECT spr round 1 (radius: 5) [00:52:04 -185115.404711] AUTODETECT spr round 2 (radius: 10) [00:54:15 -105198.443458] AUTODETECT spr round 3 (radius: 15) [00:56:30 -81739.972487] AUTODETECT spr round 4 (radius: 20) [00:59:06 -69257.148971] AUTODETECT spr round 5 (radius: 25) [01:02:26 -68311.756493] SPR radius for FAST iterations: 25 (autodetect) [01:02:26 -68311.756493] Model parameter optimization (eps = 3.000000) [01:02:40 -68292.478155] FAST spr round 1 (radius: 25) [01:04:30 -57800.341720] FAST spr round 2 (radius: 25) [01:06:02 -57321.159407] FAST spr round 3 (radius: 25) [01:07:29 -57306.029376] FAST spr round 4 (radius: 25) [01:08:49 -57291.668677] FAST spr round 5 (radius: 25) [01:10:04 -57290.460098] FAST spr round 6 (radius: 25) [01:11:18 -57290.460084] Model parameter optimization (eps = 1.000000) [01:11:31 -57288.279158] SLOW spr round 1 (radius: 5) [01:13:11 -57273.950257] SLOW spr round 2 (radius: 5) [01:14:57 -57268.207306] SLOW spr round 3 (radius: 5) [01:16:38 -57267.446632] SLOW spr round 4 (radius: 5) [01:18:17 -57267.446520] SLOW spr round 5 (radius: 10) [01:20:04 -57267.446464] SLOW spr round 6 (radius: 15) [01:22:54 -57267.446463] SLOW spr round 7 (radius: 20) [01:24:51] [worker #2] ML tree search #6, logLikelihood: -57255.542618 [01:26:46 -57267.446463] SLOW spr round 8 (radius: 25) [01:30:33] [worker #1] ML tree search #5, logLikelihood: -57231.989916 [01:31:49 -57267.446463] Model parameter optimization (eps = 0.100000) [01:31:53] [worker #0] ML tree search #4, logLikelihood: -57267.437388 [01:31:53 -410002.636638] Initial branch length optimization [01:31:57 -338144.747318] Model parameter optimization (eps = 10.000000) [01:32:34 -336205.637413] AUTODETECT spr round 1 (radius: 5) [01:34:56 -185403.405406] AUTODETECT spr round 2 (radius: 10) [01:37:15 -121467.142236] AUTODETECT spr round 3 (radius: 15) [01:39:40 -99194.607450] AUTODETECT spr round 4 (radius: 20) [01:42:36 -86536.711161] AUTODETECT spr round 5 (radius: 25) [01:45:58 -77500.672760] SPR radius for FAST iterations: 25 (autodetect) [01:45:58 -77500.672760] Model parameter optimization (eps = 3.000000) [01:46:14 -77467.208461] FAST spr round 1 (radius: 25) [01:48:15 -58610.025656] FAST spr round 2 (radius: 25) [01:49:53 -57396.003988] FAST spr round 3 (radius: 25) [01:51:25 -57291.595807] FAST spr round 4 (radius: 25) [01:52:54 -57275.067743] FAST spr round 5 (radius: 25) [01:54:15 -57275.067696] Model parameter optimization (eps = 1.000000) [01:54:29 -57267.361922] SLOW spr round 1 (radius: 5) [01:56:18 -57247.704803] SLOW spr round 2 (radius: 5) [01:58:02 -57247.683286] SLOW spr round 3 (radius: 10) [01:59:52 -57247.683208] SLOW spr round 4 (radius: 15) [02:02:42 -57247.683207] SLOW spr round 5 (radius: 20) [02:06:33 -57247.683207] SLOW spr round 6 (radius: 25) [02:10:32] [worker #2] ML tree search #9, logLikelihood: -57244.904223 [02:11:34 -57247.683207] Model parameter optimization (eps = 0.100000) [02:11:38] [worker #0] ML tree search #7, logLikelihood: -57247.668180 [02:11:39 -414544.276454] Initial branch length optimization [02:11:43 -340926.337751] Model parameter optimization (eps = 10.000000) [02:12:23 -338944.031333] AUTODETECT spr round 1 (radius: 5) [02:14:48 -185746.671290] AUTODETECT spr round 2 (radius: 10) [02:17:07 -116172.842170] AUTODETECT spr round 3 (radius: 15) [02:19:38 -92650.054826] AUTODETECT spr round 4 (radius: 20) [02:21:33] [worker #1] ML tree search #8, logLikelihood: -57244.248527 [02:22:30 -84645.697969] AUTODETECT spr round 5 (radius: 25) [02:25:44 -76403.513379] SPR radius for FAST iterations: 25 (autodetect) [02:25:44 -76403.513379] Model parameter optimization (eps = 3.000000) [02:26:02 -76380.099308] FAST spr round 1 (radius: 25) [02:28:13 -62072.546506] FAST spr round 2 (radius: 25) [02:30:08 -59128.230541] FAST spr round 3 (radius: 25) [02:31:48 -58551.736693] FAST spr round 4 (radius: 25) [02:33:13 -57619.328362] FAST spr round 5 (radius: 25) [02:34:42 -57286.812906] FAST spr round 6 (radius: 25) [02:36:04 -57269.458695] FAST spr round 7 (radius: 25) [02:37:22 -57269.458683] Model parameter optimization (eps = 1.000000) [02:37:31 -57268.078646] SLOW spr round 1 (radius: 5) [02:39:16 -57259.982504] SLOW spr round 2 (radius: 5) [02:40:57 -57259.982102] SLOW spr round 3 (radius: 10) [02:42:45 -57259.982073] SLOW spr round 4 (radius: 15) [02:45:39 -57259.982051] SLOW spr round 5 (radius: 20) [02:49:34 -57259.982031] SLOW spr round 6 (radius: 25) [02:54:01] [worker #2] ML tree search #12, logLikelihood: -57250.957142 [02:54:31 -57259.982012] Model parameter optimization (eps = 0.100000) [02:54:35] [worker #0] ML tree search #10, logLikelihood: -57259.971041 [02:54:35 -411658.593576] Initial branch length optimization [02:54:39 -336307.641294] Model parameter optimization (eps = 10.000000) [02:55:10 -334374.475870] AUTODETECT spr round 1 (radius: 5) [02:57:25 -184120.335346] AUTODETECT spr round 2 (radius: 10) [02:59:31 -112186.881152] AUTODETECT spr round 3 (radius: 15) [03:01:42 -82470.591912] AUTODETECT spr round 4 (radius: 20) [03:04:10 -72200.909868] AUTODETECT spr round 5 (radius: 25) [03:07:05 -70183.950280] SPR radius for FAST iterations: 25 (autodetect) [03:07:05 -70183.950280] Model parameter optimization (eps = 3.000000) [03:07:23 -70153.887519] FAST spr round 1 (radius: 25) [03:09:23 -58425.271595] FAST spr round 2 (radius: 25) [03:11:00 -57380.741857] FAST spr round 3 (radius: 25) [03:11:43] [worker #1] ML tree search #11, logLikelihood: -57245.847536 [03:12:31 -57306.420248] FAST spr round 4 (radius: 25) [03:13:54 -57306.419266] Model parameter optimization (eps = 1.000000) [03:14:07 -57303.626287] SLOW spr round 1 (radius: 5) [03:15:58 -57284.380230] SLOW spr round 2 (radius: 5) [03:17:42 -57281.785885] SLOW spr round 3 (radius: 5) [03:19:23 -57281.785771] SLOW spr round 4 (radius: 10) [03:21:12 -57280.804992] SLOW spr round 5 (radius: 5) [03:23:34 -57279.668757] SLOW spr round 6 (radius: 5) [03:25:33 -57279.668610] SLOW spr round 7 (radius: 10) [03:27:26 -57279.668606] SLOW spr round 8 (radius: 15) [03:30:16 -57279.668606] SLOW spr round 9 (radius: 20) [03:34:27 -57279.668606] SLOW spr round 10 (radius: 25) [03:39:45 -57279.668606] Model parameter optimization (eps = 0.100000) [03:39:49] [worker #0] ML tree search #13, logLikelihood: -57279.652114 [03:39:49 -408666.675036] Initial branch length optimization [03:39:53 -337462.620334] Model parameter optimization (eps = 10.000000) [03:40:24 -335470.951266] AUTODETECT spr round 1 (radius: 5) [03:42:36 -183387.455441] AUTODETECT spr round 2 (radius: 10) [03:42:40] [worker #2] ML tree search #15, logLikelihood: -57239.062928 [03:44:46 -115104.356602] AUTODETECT spr round 3 (radius: 15) [03:47:03 -90687.256305] AUTODETECT spr round 4 (radius: 20) [03:49:46 -74754.574301] AUTODETECT spr round 5 (radius: 25) [03:53:11 -72338.933702] SPR radius for FAST iterations: 25 (autodetect) [03:53:11 -72338.933702] Model parameter optimization (eps = 3.000000) [03:53:25 -72311.048229] FAST spr round 1 (radius: 25) [03:55:20 -61082.135848] FAST spr round 2 (radius: 25) [03:56:58 -57964.670507] FAST spr round 3 (radius: 25) [03:58:30 -57393.624309] FAST spr round 4 (radius: 25) [03:59:58 -57293.769305] FAST spr round 5 (radius: 25) [04:01:19 -57293.084326] FAST spr round 6 (radius: 25) [04:02:36 -57293.084324] Model parameter optimization (eps = 1.000000) [04:02:50 -57281.909112] SLOW spr round 1 (radius: 5) [04:03:20] [worker #1] ML tree search #14, logLikelihood: -57250.255809 [04:04:33 -57271.000458] SLOW spr round 2 (radius: 5) [04:06:15 -57269.745082] SLOW spr round 3 (radius: 5) [04:07:52 -57269.745072] SLOW spr round 4 (radius: 10) [04:09:36 -57269.745005] SLOW spr round 5 (radius: 15) [04:12:18 -57255.895433] SLOW spr round 6 (radius: 5) [04:14:37 -57255.070805] SLOW spr round 7 (radius: 5) [04:16:41 -57255.070773] SLOW spr round 8 (radius: 10) [04:18:34 -57255.070773] SLOW spr round 9 (radius: 15) [04:21:17 -57255.070773] SLOW spr round 10 (radius: 20) [04:22:29] [worker #2] ML tree search #18, logLikelihood: -57249.697813 [04:25:06 -57255.070773] SLOW spr round 11 (radius: 25) [04:30:17 -57255.070773] Model parameter optimization (eps = 0.100000) [04:30:22] [worker #0] ML tree search #16, logLikelihood: -57255.036937 [04:30:22 -413510.223525] Initial branch length optimization [04:30:27 -338021.490743] Model parameter optimization (eps = 10.000000) [04:31:21 -336116.894093] AUTODETECT spr round 1 (radius: 5) [04:33:47 -184534.499905] AUTODETECT spr round 2 (radius: 10) [04:36:03 -116116.671885] AUTODETECT spr round 3 (radius: 15) [04:38:31 -86843.789824] AUTODETECT spr round 4 (radius: 20) [04:41:20 -73817.073445] AUTODETECT spr round 5 (radius: 25) [04:44:39 -69158.208188] SPR radius for FAST iterations: 25 (autodetect) [04:44:39 -69158.208188] Model parameter optimization (eps = 3.000000) [04:44:48] [worker #1] ML tree search #17, logLikelihood: -57245.284788 [04:44:56 -69131.399297] FAST spr round 1 (radius: 25) [04:46:54 -57906.905296] FAST spr round 2 (radius: 25) [04:48:33 -57359.775452] FAST spr round 3 (radius: 25) [04:50:03 -57302.577664] FAST spr round 4 (radius: 25) [04:51:26 -57288.318378] FAST spr round 5 (radius: 25) [04:52:44 -57288.318363] Model parameter optimization (eps = 1.000000) [04:52:53 -57287.334977] SLOW spr round 1 (radius: 5) [04:54:37 -57275.174787] SLOW spr round 2 (radius: 5) [04:56:23 -57275.069914] SLOW spr round 3 (radius: 5) [04:58:09 -57275.069418] SLOW spr round 4 (radius: 10) [05:00:02 -57275.069231] SLOW spr round 5 (radius: 15) [05:02:57 -57275.069182] SLOW spr round 6 (radius: 20) [05:07:00 -57275.069182] SLOW spr round 7 (radius: 25) [05:12:13 -57275.069182] Model parameter optimization (eps = 0.100000) [05:12:17] [worker #0] ML tree search #19, logLikelihood: -57275.062332 [05:28:17] [worker #1] ML tree search #20, logLikelihood: -57236.974723 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.300068,0.427318) (0.392027,0.638875) (0.226660,1.366204) (0.081245,3.836008) 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: -57227.696492 AIC score: 118465.392984 / AICc score: 8162525.392984 / BIC score: 126412.369568 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=389). 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/Q96PU5/3_mltree/Q96PU5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.log Analysis started: 04-Jul-2021 19:39:43 / finished: 05-Jul-2021 01:08:01 Elapsed time: 19697.653 seconds Consumed energy: 1679.613 Wh (= 8 km in an electric car, or 42 km with an e-scooter!)