RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 01-Jul-2021 00:44:15 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/2_msa/O14578_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/2_msa/O14578_trimmed_msa.fasta [00:00:00] Loaded alignment with 977 taxa and 303 sites WARNING: Sequences tr_A0A1D5PK41_A0A1D5PK41_CHICK_9031 and tr_G1NC22_G1NC22_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BU01_E1BU01_CHICK_9031 and tr_G1NL00_G1NL00_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BU01_E1BU01_CHICK_9031 and tr_A0A091V7C0_A0A091V7C0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1BU01_E1BU01_CHICK_9031 and tr_A0A087R5A0_A0A087R5A0_APTFO_9233 are exactly identical! WARNING: Sequences tr_E1BU01_E1BU01_CHICK_9031 and tr_A0A093HG47_A0A093HG47_STRCA_441894 are exactly identical! WARNING: Sequences tr_E1BU01_E1BU01_CHICK_9031 and tr_A0A091WAN2_A0A091WAN2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F1NK88_F1NK88_CHICK_9031 and tr_A0A093QIW8_A0A093QIW8_9PASS_328815 are exactly identical! WARNING: Sequences tr_F1NK88_F1NK88_CHICK_9031 and tr_A0A2I0MUM6_A0A2I0MUM6_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NK88_F1NK88_CHICK_9031 and tr_A0A1V4JN14_A0A1V4JN14_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1NK88_F1NK88_CHICK_9031 and tr_A0A226N659_A0A226N659_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NUB2_F1NUB2_CHICK_9031 and tr_G1N2H3_G1N2H3_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NUB2_F1NUB2_CHICK_9031 and tr_A0A226PMR9_A0A226PMR9_COLVI_9014 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2I3HK74_A0A2I3HK74_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G1PP69_G1PP69_MYOLU_59463 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G3HUX3_G3HUX3_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G3R2B7_G3R2B7_GORGO_9595 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and sp_O77819_ROCK1_RABIT_9986 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_F1PU60_F1PU60_CANLF_9615 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2I3T6I0_A0A2I3T6I0_PANTR_9598 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_F6XUQ9_F6XUQ9_HORSE_9796 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_W5PGC0_W5PGC0_SHEEP_9940 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and sp_Q63644_ROCK1_RAT_10116 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_I3N5C1_I3N5C1_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_H0X6A1_H0X6A1_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and sp_Q13464_ROCK1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_F6T5Y1_F6T5Y1_MACMU_9544 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G5BTS2_G5BTS2_HETGA_10181 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_F7IR26_F7IR26_CALJA_9483 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_I3LFH3_I3LFH3_PIG_9823 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G1LJU8_G1LJU8_AILME_9646 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_G7PWH1_G7PWH1_MACFA_9541 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_F1MF50_F1MF50_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2I2UXM8_A0A2I2UXM8_FELCA_9685 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2I3LC55_A0A2I3LC55_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A0D9RYH3_A0A0D9RYH3_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A1S3WUE6_A0A1S3WUE6_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A1S3F137_A0A1S3F137_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2K5LSE2_A0A2K5LSE2_CERAT_9531 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2K6CYX4_A0A2K6CYX4_MACNE_9545 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2K6AB07_A0A2K6AB07_MANLE_9568 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2R9BZ53_A0A2R9BZ53_PANPA_9597 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2U4AYR8_A0A2U4AYR8_TURTR_9739 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2U3XNQ7_A0A2U3XNQ7_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A2Y9PB74_A0A2Y9PB74_DELLE_9749 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A384C1N6_A0A384C1N6_URSMA_29073 are exactly identical! WARNING: Sequences sp_P70335_ROCK1_MOUSE_10090 and tr_A0A384AW62_A0A384AW62_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q7TT50_MRCKB_MOUSE_10090 and sp_Q7TT49_MRCKB_RAT_10116 are exactly identical! WARNING: Sequences sp_Q7TT50_MRCKB_MOUSE_10090 and tr_H0WKS8_H0WKS8_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YQ38_M3YQ38_MUSPF_9669 and sp_Q28021_ROCK2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YQ38_M3YQ38_MUSPF_9669 and tr_A0A2U3W1L2_A0A2U3W1L2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YQ38_M3YQ38_MUSPF_9669 and tr_A0A2U3Y8H8_A0A2U3Y8H8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_E2R1X7_E2R1X7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_F7A5X7_F7A5X7_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_G1LQY7_G1LQY7_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_A0A2I2UU64_A0A2I2UU64_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_A0A2U3YG98_A0A2U3YG98_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_A0A2Y9JWZ2_A0A2Y9JWZ2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YWK8_M3YWK8_MUSPF_9669 and tr_A0A384CFU4_A0A384CFU4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A2I2YAK7_A0A2I2YAK7_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and sp_Q9Y5S2_MRCKB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_F7HMH6_F7HMH6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_F7F5X4_F7F5X4_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_G7PBP1_G7PBP1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A096NJX0_A0A096NJX0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A2K5KX99_A0A2K5KX99_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A2K6CZY7_A0A2K6CZY7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A2K5Z9B4_A0A2K5Z9B4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3H3V1_A0A2I3H3V1_NOMLE_61853 and tr_A0A2R9CHV9_A0A2R9CHV9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2I2ZFG1_A0A2I2ZFG1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_H2N3I5_H2N3I5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_G1TX63_G1TX63_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2I3SG77_A0A2I3SG77_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and sp_Q5VT25_MRCKA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A286ZYD7_A0A286ZYD7_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2I3LXJ5_A0A2I3LXJ5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A0D9RV25_A0A0D9RV25_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2K5MLN7_A0A2K5MLN7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2K6CDC8_A0A2K6CDC8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2K5ZJ72_A0A2K5ZJ72_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2R9AG24_A0A2R9AG24_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2U4A5D4_A0A2U4A5D4_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2Y9NQ99_A0A2Y9NQ99_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A2Y9TBZ7_A0A2Y9TBZ7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3HRA5_A0A2I3HRA5_NOMLE_61853 and tr_A0A383YX24_A0A383YX24_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1SZ34_G1SZ34_RABIT_9986 and tr_A0A2I2V5F1_A0A2I2V5F1_FELCA_9685 are exactly identical! WARNING: Sequences tr_Q29IT7_Q29IT7_DROPS_46245 and tr_B4HAM7_B4HAM7_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29IT7_Q29IT7_DROPS_46245 and tr_B4IQY4_B4IQY4_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2R2M9_H2R2M9_PANTR_9598 and sp_Q6DT37_MRCKG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R2M9_H2R2M9_PANTR_9598 and tr_A0A2R9AJ27_A0A2R9AJ27_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B806_K7B806_PANTR_9598 and sp_Q09013_DMPK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7B806_K7B806_PANTR_9598 and tr_A0A2R9CR13_A0A2R9CR13_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A3B5R5U1_A0A3B5R5U1_XIPMA_8083 and tr_A0A087Y169_A0A087Y169_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3KG87_I3KG87_ORENI_8128 and tr_A0A1S3NKA7_A0A1S3NKA7_SALSA_8030 are exactly identical! WARNING: Sequences tr_I3KG87_I3KG87_ORENI_8128 and tr_A0A2I4CK48_A0A2I4CK48_9TELE_52670 are exactly identical! WARNING: Sequences tr_I3KG87_I3KG87_ORENI_8128 and tr_A0A060X1N6_A0A060X1N6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_I3MPS2_I3MPS2_ICTTR_43179 and tr_A0A1U8C886_A0A1U8C886_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A0K0JGN2_A0A0K0JGN2_BRUMA_6279 and tr_A0A0N4TJZ8_A0A0N4TJZ8_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0JJA5_A0A0K0JJA5_BRUMA_6279 and tr_A0A158PQ70_A0A158PQ70_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A1D5QA15_A0A1D5QA15_MACMU_9544 and tr_G7PIT5_G7PIT5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QA15_A0A1D5QA15_MACMU_9544 and tr_A0A2K6AXE1_A0A2K6AXE1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_G7PPQ7_G7PPQ7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_A0A2I3NFM3_A0A2I3NFM3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_A0A0D9R4X0_A0A0D9R4X0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_A0A2K5KIC8_A0A2K5KIC8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_A0A2K6D1P3_A0A2K6D1P3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6Z971_F6Z971_MACMU_9544 and tr_A0A2K5Y1U0_A0A2K5Y1U0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5BL22_G5BL22_HETGA_10181 and tr_A0A091D4N7_A0A091D4N7_FUKDA_885580 are exactly identical! WARNING: Sequences tr_I1PX62_I1PX62_ORYGL_4538 and tr_A0A0E0PPU5_A0A0E0PPU5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1PX62_I1PX62_ORYGL_4538 and tr_A0A0D3G9N5_A0A0D3G9N5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PX62_I1PX62_ORYGL_4538 and tr_Q6L535_Q6L535_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G3SQM7_G3SQM7_LOXAF_9785 and tr_A0A2Y9QTH1_A0A2Y9QTH1_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0Z1X3_H0Z1X3_TAEGU_59729 and tr_A0A1V4JJ38_A0A1V4JJ38_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_U3ISW9_U3ISW9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_A0A093PLK1_A0A093PLK1_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_A0A091GL97_A0A091GL97_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_A0A091IDQ5_A0A091IDQ5_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_A0A218UEP4_A0A218UEP4_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZRG7_H0ZRG7_TAEGU_59729 and tr_A0A226PHZ4_A0A226PHZ4_COLVI_9014 are exactly identical! WARNING: Sequences tr_F4WAW1_F4WAW1_ACREC_103372 and tr_A0A151I4B6_A0A151I4B6_9HYME_520822 are exactly identical! WARNING: Sequences tr_F4WAW1_F4WAW1_ACREC_103372 and tr_A0A195EWD3_A0A195EWD3_9HYME_34720 are exactly identical! WARNING: Sequences tr_G0MXR2_G0MXR2_CAEBE_135651 and tr_G0PKK3_G0PKK3_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A0A1B8XYA6_A0A1B8XYA6_XENTR_8364 and tr_Q6DIL2_Q6DIL2_XENTR_8364 are exactly identical! WARNING: Sequences tr_E3LUP7_E3LUP7_CAERE_31234 and tr_A0A261BXC9_A0A261BXC9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8XUB2_A8XUB2_CAEBR_6238 and tr_A0A2G5TJZ1_A0A2G5TJZ1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A0A3Q0KR06_A0A3Q0KR06_SCHMA_6183 and tr_A0A3Q0KR10_A0A3Q0KR10_SCHMA_6183 are exactly identical! WARNING: Sequences tr_G1L1Q5_G1L1Q5_AILME_9646 and tr_A0A384BJG2_A0A384BJG2_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1MHI0_G1MHI0_AILME_9646 and tr_A0A384DJW4_A0A384DJW4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1MIQ4_G1MIQ4_AILME_9646 and tr_A0A2U3VLC1_A0A2U3VLC1_ODORO_9708 are exactly identical! WARNING: Sequences tr_L0PB67_L0PB67_PNEJ8_1209962 and tr_A0A0W4ZS12_A0A0W4ZS12_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M4ERP2_M4ERP2_BRARP_51351 and tr_A0A078I8K9_A0A078I8K9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4ERP2_M4ERP2_BRARP_51351 and tr_A0A0D3AAI2_A0A0D3AAI2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M4EUC9_M4EUC9_BRARP_51351 and tr_A0A078FC48_A0A078FC48_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4EUC9_M4EUC9_BRARP_51351 and tr_A0A0D3CEY9_A0A0D3CEY9_BRAOL_109376 are exactly identical! WARNING: Sequences tr_U3JJF0_U3JJF0_FICAL_59894 and tr_A0A3Q0FZJ0_A0A3Q0FZJ0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A091F4A6_A0A091F4A6_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A091IQF0_A0A091IQF0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A091VQN4_A0A091VQN4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A087RE81_A0A087RE81_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A099ZCX1_A0A099ZCX1_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A093GA35_A0A093GA35_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3KAH6_U3KAH6_FICAL_59894 and tr_A0A218UJG9_A0A218UJG9_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A0Q3R9S9_A0A0Q3R9S9_AMAAE_12930 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A091JRJ8_A0A091JRJ8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A093Q7X2_A0A093Q7X2_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A093HKK8_A0A093HKK8_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A091VTF3_A0A091VTF3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A0A0AL22_A0A0A0AL22_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A2I0MW50_A0A2I0MW50_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A091I6L8_A0A091I6L8_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3I4S8_U3I4S8_ANAPL_8839 and tr_A0A218V1C6_A0A218V1C6_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3IVP2_U3IVP2_ANAPL_8839 and tr_A0A091G1Z5_A0A091G1Z5_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3IVP2_U3IVP2_ANAPL_8839 and tr_A0A0A0AT85_A0A0A0AT85_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U5H6D2_U5H6D2_USTV1_683840 and tr_A0A2X0P087_A0A2X0P087_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XUG5_V2XUG5_MONRO_1381753 and tr_A0A0W0FZG3_A0A0W0FZG3_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A3B5XXY3_A0A3B5XXY3_WHEAT_4565 and tr_A0A3B5ZR05_A0A3B5ZR05_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A158N7Z8_A0A158N7Z8_ONCVO_6282 and tr_A0A182DYX1_A0A182DYX1_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067GWQ9_A0A067GWQ9_CITSI_2711 and tr_V4SJT8_V4SJT8_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GWQ9_A0A067GWQ9_CITSI_2711 and tr_A0A2H5NHE9_A0A2H5NHE9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A074S073_A0A074S073_9HOMO_1423351 and tr_A0A0K6FVP8_A0A0K6FVP8_9HOMO_456999 are exactly identical! WARNING: Sequences tr_A0A0D9S4G6_A0A0D9S4G6_CHLSB_60711 and tr_A0A2K5LKY4_A0A2K5LKY4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S4G6_A0A0D9S4G6_CHLSB_60711 and tr_A0A2K5Y543_A0A2K5Y543_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0LNF7_A0A0A0LNF7_CUCSA_3659 and tr_A0A1S3BA95_A0A1S3BA95_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4RZX4_V4RZX4_9ROSI_85681 and tr_A0A2H5Q7X1_A0A2H5Q7X1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A091JRS4_A0A091JRS4_EGRGA_188379 and tr_A0A1V4KAN3_A0A1V4KAN3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A194R8N7_A0A194R8N7_PAPMA_76193 and tr_A0A194PPF9_A0A194PPF9_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0C9MKS2_A0A0C9MKS2_9FUNG_91626 and tr_A0A168PK75_A0A168PK75_MUCCL_747725 are exactly identical! WARNING: Sequences tr_A0A0C9ZD94_A0A0C9ZD94_9HOMO_765257 and tr_A0A0C3PAW0_A0A0C3PAW0_PISTI_870435 are exactly identical! WARNING: Sequences tr_A0A0V0RV22_A0A0V0RV22_9BILA_6336 and tr_A0A0V1CXA9_A0A0V1CXA9_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RV22_A0A0V0RV22_9BILA_6336 and tr_A0A0V0U539_A0A0V0U539_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0RYB8_A0A0V0RYB8_9BILA_6336 and tr_A0A0V1DIC8_A0A0V1DIC8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RYB8_A0A0V0RYB8_9BILA_6336 and tr_A0A0V0XAG5_A0A0V0XAG5_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RYB8_A0A0V0RYB8_9BILA_6336 and tr_A0A0V0VR42_A0A0V0VR42_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RYB8_A0A0V0RYB8_9BILA_6336 and tr_A0A0V1A1N7_A0A0V1A1N7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RYB8_A0A0V0RYB8_9BILA_6336 and tr_A0A0V1P6Z6_A0A0V1P6Z6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1LF44_A0A0V1LF44_9BILA_6335 and tr_A0A0V1PHM5_A0A0V1PHM5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1M6H9_A0A0V1M6H9_9BILA_268474 and tr_A0A0V1HW26_A0A0V1HW26_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1MMM9_A0A0V1MMM9_9BILA_268474 and tr_A0A0V1HUS0_A0A0V1HUS0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A164Z6G0_A0A164Z6G0_9HOMO_1314777 and tr_A0A166EIA9_A0A166EIA9_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JV62_A0A1S3JV62_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JV95_A0A1S3JV95_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JV97_A0A1S3JV97_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JVF2_A0A1S3JVF2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JW34_A0A1S3JW34_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV58_A0A1S3JV58_LINUN_7574 and tr_A0A1S3JW59_A0A1S3JW59_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3R664_A0A1S3R664_SALSA_8030 and tr_A0A060VUS1_A0A060VUS1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7UMW1_A0A1I7UMW1_9PELO_1561998 and tr_A0A1I7UMW2_A0A1I7UMW2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226MKY1_A0A226MKY1_CALSU_9009 and tr_A0A226NV79_A0A226NV79_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MT22_A0A226MT22_CALSU_9009 and tr_A0A226PNJ8_A0A226PNJ8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PR40_A0A2D0PR40_ICTPU_7998 and tr_A0A2D0PTT9_A0A2D0PTT9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R7D9_A0A2D0R7D9_ICTPU_7998 and tr_A0A2D0R7E3_A0A2D0R7E3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RMQ7_A0A2D0RMQ7_ICTPU_7998 and tr_A0A2D0RNR4_A0A2D0RNR4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRV8_A0A2D0SRV8_ICTPU_7998 and tr_A0A2D0SRW1_A0A2D0SRW1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRV8_A0A2D0SRV8_ICTPU_7998 and tr_A0A2D0SRW3_A0A2D0SRW3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRV8_A0A2D0SRV8_ICTPU_7998 and tr_A0A2D0SSF8_A0A2D0SSF8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRV8_A0A2D0SRV8_ICTPU_7998 and tr_A0A2D0SSZ9_A0A2D0SSZ9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G2YUY4_A0A2G2YUY4_CAPAN_4072 and tr_A0A2G3BNX9_A0A2G3BNX9_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5P066_A0A2K5P066_CERAT_9531 and tr_A0A2K5ZSQ5_A0A2K5ZSQ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U1MLD5_A0A2U1MLD5_ARTAN_35608 and tr_A0A2U1NQZ6_A0A2U1NQZ6_ARTAN_35608 are exactly identical! WARNING: Sequences tr_A0A2U3ZG98_A0A2U3ZG98_ODORO_9708 and tr_A0A2U3Z3T6_A0A2U3Z3T6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 199 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/O14578/3_mltree/O14578.raxml.reduced.phy Alignment comprises 1 partitions and 303 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 303 / 303 Gaps: 2.89 % Invariant sites: 0.99 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 977 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 303 / 24240 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -399085.066651] Initial branch length optimization [00:00:06 -333173.415782] Model parameter optimization (eps = 10.000000) [00:01:09 -331514.830763] AUTODETECT spr round 1 (radius: 5) [00:05:01 -199024.829700] AUTODETECT spr round 2 (radius: 10) [00:09:01 -135206.392467] AUTODETECT spr round 3 (radius: 15) [00:13:09 -103472.352304] AUTODETECT spr round 4 (radius: 20) [00:18:02 -92806.177925] AUTODETECT spr round 5 (radius: 25) [00:24:38 -87361.402993] SPR radius for FAST iterations: 25 (autodetect) [00:24:38 -87361.402993] Model parameter optimization (eps = 3.000000) [00:25:00 -87351.717422] FAST spr round 1 (radius: 25) [00:28:33 -73444.520047] FAST spr round 2 (radius: 25) [00:31:18 -72806.737010] FAST spr round 3 (radius: 25) [00:33:47 -72760.834779] FAST spr round 4 (radius: 25) [00:35:58 -72756.674053] FAST spr round 5 (radius: 25) [00:38:02 -72756.673547] Model parameter optimization (eps = 1.000000) [00:38:14 -72755.941739] SLOW spr round 1 (radius: 5) [00:40:53 -72738.425582] SLOW spr round 2 (radius: 5) [00:43:35 -72731.647847] SLOW spr round 3 (radius: 5) [00:46:19 -72731.645189] SLOW spr round 4 (radius: 10) [00:49:15 -72731.643485] SLOW spr round 5 (radius: 15) [00:54:17 -72731.642477] SLOW spr round 6 (radius: 20) [01:02:31 -72731.641857] SLOW spr round 7 (radius: 25) [01:14:03 -72729.487957] SLOW spr round 8 (radius: 5) [01:14:19] [worker #4] ML tree search #5, logLikelihood: -72744.729938 [01:17:26] [worker #1] ML tree search #2, logLikelihood: -72713.345111 [01:18:10 -72729.200887] SLOW spr round 9 (radius: 5) [01:21:42 -72729.200681] SLOW spr round 10 (radius: 10) [01:24:42 -72729.200581] SLOW spr round 11 (radius: 15) [01:26:18] [worker #3] ML tree search #4, logLikelihood: -72729.056102 [01:29:33 -72729.200495] SLOW spr round 12 (radius: 20) [01:37:46 -72729.200337] SLOW spr round 13 (radius: 25) [01:49:15 -72729.200278] Model parameter optimization (eps = 0.100000) [01:49:29] [worker #0] ML tree search #1, logLikelihood: -72729.013388 [01:49:29 -405750.001772] Initial branch length optimization [01:49:35 -338536.766219] Model parameter optimization (eps = 10.000000) [01:50:37 -336688.024228] AUTODETECT spr round 1 (radius: 5) [01:54:30 -196611.577136] AUTODETECT spr round 2 (radius: 10) [01:58:26 -134695.939319] AUTODETECT spr round 3 (radius: 15) [02:01:56] [worker #2] ML tree search #3, logLikelihood: -72732.299127 [02:02:54 -104508.172344] AUTODETECT spr round 4 (radius: 20) [02:08:09 -87063.558539] AUTODETECT spr round 5 (radius: 25) [02:14:20 -85025.255342] SPR radius for FAST iterations: 25 (autodetect) [02:14:20 -85025.255342] Model parameter optimization (eps = 3.000000) [02:14:46 -85016.171267] FAST spr round 1 (radius: 25) [02:18:10 -73774.543758] FAST spr round 2 (radius: 25) [02:21:02 -72847.464655] FAST spr round 3 (radius: 25) [02:23:29 -72747.377344] FAST spr round 4 (radius: 25) [02:25:44 -72740.590018] FAST spr round 5 (radius: 25) [02:27:46 -72740.588164] Model parameter optimization (eps = 1.000000) [02:28:06 -72739.293580] SLOW spr round 1 (radius: 5) [02:30:50 -72724.850507] SLOW spr round 2 (radius: 5) [02:30:52] [worker #4] ML tree search #10, logLikelihood: -72719.398546 [02:33:32 -72723.725323] SLOW spr round 3 (radius: 5) [02:36:17 -72723.101132] SLOW spr round 4 (radius: 5) [02:39:01 -72722.927542] SLOW spr round 5 (radius: 5) [02:41:41 -72722.927477] SLOW spr round 6 (radius: 10) [02:44:33 -72722.927424] SLOW spr round 7 (radius: 15) [02:49:31 -72722.927371] SLOW spr round 8 (radius: 20) [02:57:08 -72722.927315] SLOW spr round 9 (radius: 25) [03:08:10 -72722.927257] Model parameter optimization (eps = 0.100000) [03:08:14] [worker #3] ML tree search #9, logLikelihood: -72723.256078 [03:08:16] [worker #0] ML tree search #6, logLikelihood: -72722.907535 [03:08:16 -399822.025523] Initial branch length optimization [03:08:22 -333523.218667] Model parameter optimization (eps = 10.000000) [03:09:39 -331990.948256] AUTODETECT spr round 1 (radius: 5) [03:13:44 -199681.340725] AUTODETECT spr round 2 (radius: 10) [03:17:41 -136062.717442] AUTODETECT spr round 3 (radius: 15) [03:22:07 -107864.278760] AUTODETECT spr round 4 (radius: 20) [03:22:31] [worker #1] ML tree search #7, logLikelihood: -72738.278626 [03:27:54 -94151.132625] AUTODETECT spr round 5 (radius: 25) [03:34:29 -89159.385213] SPR radius for FAST iterations: 25 (autodetect) [03:34:29 -89159.385213] Model parameter optimization (eps = 3.000000) [03:34:52 -89153.540216] FAST spr round 1 (radius: 25) [03:38:52 -73808.426847] FAST spr round 2 (radius: 25) [03:41:38 -72882.956718] FAST spr round 3 (radius: 25) [03:44:09 -72812.395731] FAST spr round 4 (radius: 25) [03:46:22 -72794.771561] FAST spr round 5 (radius: 25) [03:48:23 -72794.770603] Model parameter optimization (eps = 1.000000) [03:48:43 -72793.333660] SLOW spr round 1 (radius: 5) [03:50:37] [worker #2] ML tree search #8, logLikelihood: -72726.289866 [03:51:27 -72768.770114] SLOW spr round 2 (radius: 5) [03:54:14 -72765.633634] SLOW spr round 3 (radius: 5) [03:57:01 -72765.263353] SLOW spr round 4 (radius: 5) [03:59:46 -72765.261444] SLOW spr round 5 (radius: 10) [04:02:42 -72765.260589] SLOW spr round 6 (radius: 15) [04:07:23 -72765.260179] SLOW spr round 7 (radius: 20) [04:14:26 -72765.260022] SLOW spr round 8 (radius: 25) [04:23:16] [worker #3] ML tree search #14, logLikelihood: -72716.186301 [04:24:26 -72765.080425] SLOW spr round 9 (radius: 5) [04:28:30 -72765.076830] SLOW spr round 10 (radius: 10) [04:32:13 -72765.076080] SLOW spr round 11 (radius: 15) [04:36:46 -72763.146322] SLOW spr round 12 (radius: 5) [04:40:42 -72763.146015] SLOW spr round 13 (radius: 10) [04:42:20] [worker #1] ML tree search #12, logLikelihood: -72737.409999 [04:42:54] [worker #4] ML tree search #15, logLikelihood: -72713.712172 [04:44:09 -72763.145863] SLOW spr round 14 (radius: 15) [04:48:41 -72763.145737] SLOW spr round 15 (radius: 20) [04:56:05 -72763.145631] SLOW spr round 16 (radius: 25) [05:06:10 -72762.860232] SLOW spr round 17 (radius: 5) [05:10:16 -72762.802514] SLOW spr round 18 (radius: 10) [05:13:54 -72762.801160] SLOW spr round 19 (radius: 15) [05:15:27] [worker #2] ML tree search #13, logLikelihood: -72719.002377 [05:18:20 -72762.800329] SLOW spr round 20 (radius: 20) [05:25:35 -72762.799906] SLOW spr round 21 (radius: 25) [05:35:28 -72762.799689] Model parameter optimization (eps = 0.100000) [05:35:40] [worker #0] ML tree search #11, logLikelihood: -72762.669754 [05:35:40 -400043.041544] Initial branch length optimization [05:35:49 -334033.201489] Model parameter optimization (eps = 10.000000) [05:36:43 -332412.909835] AUTODETECT spr round 1 (radius: 5) [05:40:39 -200951.433971] AUTODETECT spr round 2 (radius: 10) [05:44:42 -136371.785613] AUTODETECT spr round 3 (radius: 15) [05:48:55 -109809.676133] AUTODETECT spr round 4 (radius: 20) [05:52:42] [worker #3] ML tree search #19, logLikelihood: -72725.872932 [05:53:35 -96803.328358] AUTODETECT spr round 5 (radius: 25) [05:59:41 -90757.494249] SPR radius for FAST iterations: 25 (autodetect) [05:59:41 -90757.494249] Model parameter optimization (eps = 3.000000) [06:00:07 -90750.478612] FAST spr round 1 (radius: 25) [06:03:44 -74216.593891] FAST spr round 2 (radius: 25) [06:06:18 -72876.470390] FAST spr round 3 (radius: 25) [06:08:45 -72755.626744] FAST spr round 4 (radius: 25) [06:10:54 -72752.435795] FAST spr round 5 (radius: 25) [06:12:55 -72752.435670] Model parameter optimization (eps = 1.000000) [06:13:04 -72752.181864] SLOW spr round 1 (radius: 5) [06:15:49 -72726.321360] SLOW spr round 2 (radius: 5) [06:18:30 -72724.957516] SLOW spr round 3 (radius: 5) [06:21:06 -72723.871680] SLOW spr round 4 (radius: 5) [06:23:43 -72723.871200] SLOW spr round 5 (radius: 10) [06:25:29] [worker #4] ML tree search #20, logLikelihood: -72726.696218 [06:26:32 -72723.870852] SLOW spr round 6 (radius: 15) [06:31:32 -72723.870609] SLOW spr round 7 (radius: 20) [06:32:30] [worker #2] ML tree search #18, logLikelihood: -72730.979680 [06:39:28 -72723.870427] SLOW spr round 8 (radius: 25) [06:50:51 -72723.870287] Model parameter optimization (eps = 0.100000) [06:50:58] [worker #0] ML tree search #16, logLikelihood: -72723.830777 [07:07:19] [worker #1] ML tree search #17, logLikelihood: -72733.769888 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.245248,0.340331) (0.330753,0.452549) (0.277684,1.165828) (0.146315,3.028538) 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: -72713.345111 AIC score: 149340.690221 / AICc score: 7812952.690221 / BIC score: 156608.465322 Free parameters (model + branch lengths): 1957 WARNING: Number of free parameters (K=1957) is larger than alignment size (n=303). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 263 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14578/3_mltree/O14578.raxml.log Analysis started: 01-Jul-2021 00:44:15 / finished: 01-Jul-2021 07:51:35 Elapsed time: 25639.711 seconds Consumed energy: 2377.424 Wh (= 12 km in an electric car, or 59 km with an e-scooter!)