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 15:48:19 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/2_msa/Q96QI5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/3_mltree/Q96QI5 --seed 2 --threads 4 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/2_msa/Q96QI5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 189 sites WARNING: Sequences tr_B4NUQ3_B4NUQ3_DROSI_7240 and tr_B4I734_B4I734_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NW64_A0A1D5NW64_CHICK_9031 and tr_A0A226NMW5_A0A226NMW5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5NW64_A0A1D5NW64_CHICK_9031 and tr_A0A226PQQ7_A0A226PQQ7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PIC5_A0A1D5PIC5_CHICK_9031 and tr_A0A226PQA8_A0A226PQA8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PZZ4_A0A1D5PZZ4_CHICK_9031 and tr_F1NL56_F1NL56_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1D5PZZ4_A0A1D5PZZ4_CHICK_9031 and tr_A0A226MN89_A0A226MN89_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PZZ4_A0A1D5PZZ4_CHICK_9031 and tr_A0A226MSX8_A0A226MSX8_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PZZ4_A0A1D5PZZ4_CHICK_9031 and tr_A0A226PMF2_A0A226PMF2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PZZ4_A0A1D5PZZ4_CHICK_9031 and tr_A0A226PNV0_A0A226PNV0_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1C4I5_E1C4I5_CHICK_9031 and tr_A0A226NHJ6_A0A226NHJ6_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NW51_F1NW51_CHICK_9031 and tr_A0A218UCX8_A0A218UCX8_9PASE_299123 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_G1NL03_G1NL03_MELGA_9103 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_H0ZNZ3_H0ZNZ3_TAEGU_59729 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_U3K8V3_U3K8V3_FICAL_59894 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_R0M3Y6_R0M3Y6_ANAPL_8839 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A0Q3UR62_A0A0Q3UR62_AMAAE_12930 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A093QF61_A0A093QF61_9PASS_328815 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A091VMF4_A0A091VMF4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A087RKY3_A0A087RKY3_APTFO_9233 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A099ZML2_A0A099ZML2_TINGU_94827 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A2I0MUD6_A0A2I0MUD6_COLLI_8932 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A091IR97_A0A091IR97_CALAN_9244 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A1V4JLU6_A0A1V4JLU6_PATFA_372326 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A218UX55_A0A218UX55_9PASE_299123 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A226MI74_A0A226MI74_CALSU_9009 are exactly identical! WARNING: Sequences tr_R4GJI3_R4GJI3_CHICK_9031 and tr_A0A226PAL8_A0A226PAL8_COLVI_9014 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A2I3H788_A0A2I3H788_NOMLE_61853 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_G3I6K5_G3I6K5_CRIGR_10029 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_G3R2K0_G3R2K0_GORGO_9595 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_H2NQG4_H2NQG4_PONAB_9601 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_G1TEE5_G1TEE5_RABIT_9986 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A2I3SIJ1_A0A2I3SIJ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A1D5QQK4_A0A1D5QQK4_MACMU_9544 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_F7HZT9_F7HZT9_CALJA_9483 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A096MY37_A0A096MY37_PAPAN_9555 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A2K5L8W4_A0A2K5L8W4_CERAT_9531 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A2K6A3T7_A0A2K6A3T7_MANLE_9568 are exactly identical! WARNING: Sequences tr_D3YVV6_D3YVV6_MOUSE_10090 and tr_A0A2R9BV73_A0A2R9BV73_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q673U1_HS3S2_MOUSE_10090 and tr_G3IAT6_G3IAT6_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q673U1_HS3S2_MOUSE_10090 and sp_Q80W66_HS3S2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BKN6_HS3SA_MOUSE_10090 and tr_D3ZFR1_D3ZFR1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BKN6_HS3SA_MOUSE_10090 and tr_D3ZTA9_D3ZTA9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_M3YFU5_M3YFU5_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_G3HHV9_G3HHV9_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_G1SI81_G1SI81_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_E2QTV5_E2QTV5_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_W5PI73_W5PI73_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_I3MWX3_I3MWX3_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_G3T631_G3T631_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_G3WJQ9_G3WJQ9_SARHA_9305 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_D2HKE9_D2HKE9_AILME_9646 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_Q0VD21_Q0VD21_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_M3WSU2_M3WSU2_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A1S3GJ60_A0A1S3GJ60_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A2U4AV05_A0A2U4AV05_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A2U3VRZ2_A0A2U3VRZ2_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A2U3YIH2_A0A2U3YIH2_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A2Y9L3G1_A0A2Y9L3G1_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A2Y9F5X5_A0A2Y9F5X5_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8BSL4_HS3S5_MOUSE_10090 and tr_A0A384DC86_A0A384DC86_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XWN5_M3XWN5_MUSPF_9669 and tr_A0A2Y9L5R7_A0A2Y9L5R7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XWN5_M3XWN5_MUSPF_9669 and tr_A0A2Y9LFZ2_A0A2Y9LFZ2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YZC2_M3YZC2_MUSPF_9669 and tr_A0A2Y9L8A6_A0A2Y9L8A6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_G3RFC1_G3RFC1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_H2NQE0_H2NQE0_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_H2QAR3_H2QAR3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_F7DEU8_F7DEU8_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and sp_Q9Y278_HS3S2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_U3DRC6_U3DRC6_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_G7Q0Q0_G7Q0Q0_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A096NHD6_A0A096NHD6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A0D9R3M4_A0A0D9R3M4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A1U7TBH0_A0A1U7TBH0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A2K5N5Q6_A0A2K5N5Q6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A2K6CDE8_A0A2K6CDE8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A2K5ZAU0_A0A2K5ZAU0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3FS76_A0A2I3FS76_NOMLE_61853 and tr_A0A2R9B8Q8_A0A2R9B8Q8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_G3QFL4_G3QFL4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2J8U159_A0A2J8U159_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2I3TTT2_A0A2I3TTT2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_F6YIP3_F6YIP3_MONDO_13616 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and sp_Q8IZT8_HS3S5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_F7IAJ7_F7IAJ7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_G7P3M0_G7P3M0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_L5JMT8_L5JMT8_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A096MX52_A0A096MX52_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A0D9RT36_A0A0D9RT36_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2K5L8U9_A0A2K5L8U9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2K6BWI1_A0A2K6BWI1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2K5XKT5_A0A2K5XKT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RRJ5_G1RRJ5_NOMLE_61853 and tr_A0A2R8ZRJ5_A0A2R8ZRJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_G1RX19_G1RX19_NOMLE_61853 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_G3SF27_G3SF27_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_H2R151_H2R151_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and sp_Q9Y662_HS3SB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and sp_Q9Y663_HS3SA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_F7H338_F7H338_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2R8PMI3_A0A2R8PMI3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_G7PIY8_G7PIY8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_G7PTQ2_G7PTQ2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A096P2Y9_A0A096P2Y9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A096P2Z1_A0A096P2Z1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A0D9R9H6_A0A0D9R9H6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K5MYP5_A0A2K5MYP5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K5P3K2_A0A2K5P3K2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K6BT35_A0A2K6BT35_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K6E6N3_A0A2K6E6N3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K5XQD2_A0A2K5XQD2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2K5YN88_A0A2K5YN88_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RX13_G1RX13_NOMLE_61853 and tr_A0A2R9CLN9_A0A2R9CLN9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RXI3_G3RXI3_GORGO_9595 and tr_H2NST3_H2NST3_PONAB_9601 are exactly identical! WARNING: Sequences tr_H2PCX6_H2PCX6_PONAB_9601 and tr_H2QP83_H2QP83_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PCX6_H2PCX6_PONAB_9601 and sp_O14792_HS3S1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PCX6_H2PCX6_PONAB_9601 and tr_A0A2R8ZDV3_A0A2R8ZDV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NQY4_G1NQY4_MELGA_9103 and tr_A0A091UKI3_A0A091UKI3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1NQY4_G1NQY4_MELGA_9103 and tr_A0A0A0ANY3_A0A0A0ANY3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1T3A3_G1T3A3_RABIT_9986 and tr_G1T571_G1T571_RABIT_9986 are exactly identical! WARNING: Sequences tr_F1P9J1_F1P9J1_CANLF_9615 and tr_J9NRZ8_J9NRZ8_CANLF_9615 are exactly identical! WARNING: Sequences tr_J9NVS2_J9NVS2_CANLF_9615 and tr_A0A2U3Z0H9_A0A2U3Z0H9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_J9NVS2_J9NVS2_CANLF_9615 and tr_A0A384CLS0_A0A384CLS0_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3T3Q8_A0A2I3T3Q8_PANTR_9598 and tr_A0A2R9A8E4_A0A2R9A8E4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6PWA0_F6PWA0_MONDO_13616 and tr_G3W5L4_G3W5L4_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6YUM6_F6YUM6_MONDO_13616 and tr_G3WNW0_G3WNW0_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6PP00_F6PP00_HORSE_9796 and tr_A0A286XPL5_A0A286XPL5_CAVPO_10141 are exactly identical! WARNING: Sequences tr_F6PP00_F6PP00_HORSE_9796 and tr_A0A1U7QUH0_A0A1U7QUH0_MESAU_10036 are exactly identical! WARNING: Sequences tr_F6SM40_F6SM40_HORSE_9796 and tr_F6SM58_F6SM58_HORSE_9796 are exactly identical! WARNING: Sequences tr_W5PM60_W5PM60_SHEEP_9940 and tr_A0A1U7UCM3_A0A1U7UCM3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_W5Q4A2_W5Q4A2_SHEEP_9940 and tr_E1BKQ1_E1BKQ1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q4A2_W5Q4A2_SHEEP_9940 and tr_A0A2U4A8M6_A0A2U4A8M6_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5Q4A2_W5Q4A2_SHEEP_9940 and tr_A0A2Y9PEE9_A0A2Y9PEE9_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5Q4A2_W5Q4A2_SHEEP_9940 and tr_A0A2Y9SM67_A0A2Y9SM67_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5Q4A2_W5Q4A2_SHEEP_9940 and tr_A0A384BGD3_A0A384BGD3_BALAS_310752 are exactly identical! WARNING: Sequences tr_W5Q4M4_W5Q4M4_SHEEP_9940 and tr_E1BNJ7_E1BNJ7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5PQE1_A0A3B5PQE1_XIPMA_8083 and tr_A0A087YHK0_A0A087YHK0_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5PZD6_A0A3B5PZD6_XIPMA_8083 and tr_A0A087Y0Z4_A0A087Y0Z4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5Q3D2_A0A3B5Q3D2_XIPMA_8083 and tr_A0A087YAN6_A0A087YAN6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5RBH5_A0A3B5RBH5_XIPMA_8083 and tr_A0A087YAI1_A0A087YAI1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5RBH5_A0A3B5RBH5_XIPMA_8083 and tr_A0A2I4D618_A0A2I4D618_9TELE_52670 are exactly identical! WARNING: Sequences tr_M4A4T6_M4A4T6_XIPMA_8083 and tr_A0A087Y103_A0A087Y103_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NCP8_A0A158NCP8_ATTCE_12957 and tr_A0A195BWN3_A0A195BWN3_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NEG2_A0A158NEG2_ATTCE_12957 and tr_A0A195BWY8_A0A195BWY8_9HYME_520822 are exactly identical! WARNING: Sequences tr_H0X3X6_H0X3X6_OTOGA_30611 and tr_A0A384ATQ9_A0A384ATQ9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A0H5SMJ3_A0A0H5SMJ3_BRUMA_6279 and tr_A0A158PSC9_A0A158PSC9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_G7P5A0_G7P5A0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_A0A096MMR1_A0A096MMR1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_A0A0D9SEA6_A0A0D9SEA6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_A0A2K5L1C5_A0A2K5L1C5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_A0A2K6B061_A0A2K6B061_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DQN3_F7DQN3_MACMU_9544 and tr_A0A2K5XUR4_A0A2K5XUR4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5BRA4_G5BRA4_HETGA_10181 and tr_G5C1H5_G5C1H5_HETGA_10181 are exactly identical! WARNING: Sequences tr_G5BRA4_G5BRA4_HETGA_10181 and tr_A0A091DTU9_A0A091DTU9_FUKDA_885580 are exactly identical! WARNING: Sequences tr_E5S1L4_E5S1L4_TRISP_6334 and tr_A0A0V0VBE7_A0A0V0VBE7_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5S1L4_E5S1L4_TRISP_6334 and tr_A0A0V0ZNY9_A0A0V0ZNY9_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5S1L4_E5S1L4_TRISP_6334 and tr_A0A0V0UDE4_A0A0V0UDE4_9BILA_144512 are exactly identical! WARNING: Sequences tr_G3TMZ4_G3TMZ4_LOXAF_9785 and tr_G3U2C7_G3U2C7_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H0Z3N2_H0Z3N2_TAEGU_59729 and tr_H1A5P3_H1A5P3_TAEGU_59729 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_U3KL15_U3KL15_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A091EAX4_A0A091EAX4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A093PIZ9_A0A093PIZ9_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A218V8P4_A0A218V8P4_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WVJ3_F4WVJ3_ACREC_103372 and tr_A0A195FL99_A0A195FL99_9HYME_34720 are exactly identical! WARNING: Sequences tr_F4WVJ3_F4WVJ3_ACREC_103372 and tr_A0A195CPV1_A0A195CPV1_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A287A1I4_A0A287A1I4_PIG_9823 and tr_A0A287A8H4_A0A287A8H4_PIG_9823 are exactly identical! WARNING: Sequences tr_H3BE49_H3BE49_LATCH_7897 and tr_M3XH41_M3XH41_LATCH_7897 are exactly identical! WARNING: Sequences tr_G1MKU9_G1MKU9_AILME_9646 and tr_A0A2U3VQ42_A0A2U3VQ42_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1MKU9_G1MKU9_AILME_9646 and tr_A0A2U3XZB6_A0A2U3XZB6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1MKU9_G1MKU9_AILME_9646 and tr_A0A2Y9LKZ6_A0A2Y9LKZ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_R7UHG2_R7UHG2_CAPTE_283909 and tr_R7V4J2_R7V4J2_CAPTE_283909 are exactly identical! WARNING: Sequences tr_U3JD84_U3JD84_FICAL_59894 and tr_U3K4I6_U3K4I6_FICAL_59894 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A091J234_A0A091J234_EGRGA_188379 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A093S712_A0A093S712_9PASS_328815 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A091ULV8_A0A091ULV8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A087QGU4_A0A087QGU4_APTFO_9233 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A093GUM2_A0A093GUM2_STRCA_441894 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A091XR62_A0A091XR62_OPIHO_30419 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A099YW58_A0A099YW58_TINGU_94827 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A099Z558_A0A099Z558_TINGU_94827 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A091GE52_A0A091GE52_9AVES_55661 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A0A0A3J7_A0A0A0A3J7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_R0KSD1_R0KSD1_ANAPL_8839 and tr_A0A2I0M752_A0A2I0M752_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A091EQL8_A0A091EQL8_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A093QKK4_A0A093QKK4_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A087RGA6_A0A087RGA6_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A091XU95_A0A091XU95_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A091GF50_A0A091GF50_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A099ZYZ9_A0A099ZYZ9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A091HK64_A0A091HK64_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A226NNC0_A0A226NNC0_CALSU_9009 are exactly identical! WARNING: Sequences tr_U3I235_U3I235_ANAPL_8839 and tr_A0A226PQZ2_A0A226PQZ2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A0N4TSI8_A0A0N4TSI8_BRUPA_6280 and tr_A0A0R3QZ00_A0A0R3QZ00_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A151M262_A0A151M262_ALLMI_8496 and tr_A0A3Q0H0U9_A0A3Q0H0U9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151N226_A0A151N226_ALLMI_8496 and tr_A0A1U7RUC7_A0A1U7RUC7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NZF6_A0A151NZF6_ALLMI_8496 and tr_A0A1U7SK21_A0A1U7SK21_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ELT9_A0A091ELT9_CORBR_85066 and tr_A0A093Q7H3_A0A093Q7H3_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091ISK6_A0A091ISK6_EGRGA_188379 and tr_A0A091WEC1_A0A091WEC1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091ISK6_A0A091ISK6_EGRGA_188379 and tr_A0A099ZUT6_A0A099ZUT6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091ISK6_A0A091ISK6_EGRGA_188379 and tr_A0A091HKF3_A0A091HKF3_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0LX16_A0A2I0LX16_COLLI_8932 and tr_A0A1V4KSY3_A0A1V4KSY3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MM37_A0A2I0MM37_COLLI_8932 and tr_A0A1V4JFD8_A0A1V4JFD8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CCG7_A0A0V1CCG7_TRIBR_45882 and tr_A0A0V0WQ61_A0A0V0WQ61_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CCG7_A0A0V1CCG7_TRIBR_45882 and tr_A0A0V1L9P6_A0A0V1L9P6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CCG7_A0A0V1CCG7_TRIBR_45882 and tr_A0A0V0TA96_A0A0V0TA96_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WNJ7_A0A0V0WNJ7_9BILA_92179 and tr_A0A0V1LCY0_A0A0V1LCY0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1M5I0_A0A0V1M5I0_9BILA_268474 and tr_A0A0V1HWY4_A0A0V1HWY4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3EVS3_A0A1S3EVS3_DIPOR_10020 and tr_A0A1S3EZ09_A0A1S3EZ09_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A1S3R9U0_A0A1S3R9U0_SALSA_8030 and tr_A0A060XGG5_A0A060XGG5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S638_A0A1S3S638_SALSA_8030 and tr_A0A060YWG5_A0A060YWG5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S803_A0A1S3S803_SALSA_8030 and tr_A0A060WQW0_A0A060WQW0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7UA92_A0A1I7UA92_9PELO_1561998 and tr_A0A1I7UA93_A0A1I7UA93_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7UA92_A0A1I7UA92_9PELO_1561998 and tr_A0A1I7UA94_A0A1I7UA94_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1U7T8J5_A0A1U7T8J5_TARSY_1868482 and tr_A0A1U7UTQ9_A0A1U7UTQ9_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1U7QAG1_A0A1U7QAG1_MESAU_10036 and tr_A0A3Q0CG61_A0A3Q0CG61_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A060X803_A0A060X803_ONCMY_8022 and tr_A0A060Y216_A0A060Y216_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A218UGN0_A0A218UGN0_9PASE_299123 and tr_A0A218UI65_A0A218UI65_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2U3V7N4_A0A2U3V7N4_TURTR_9739 and tr_A0A2Y9MP20_A0A2Y9MP20_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A8M0_A0A2U4A8M0_TURTR_9739 and tr_A0A2Y9PB65_A0A2Y9PB65_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A8M0_A0A2U4A8M0_TURTR_9739 and tr_A0A2Y9SUA7_A0A2Y9SUA7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4C2S2_A0A2U4C2S2_TURTR_9739 and tr_A0A2Y9M3F2_A0A2Y9M3F2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C2S2_A0A2U4C2S2_TURTR_9739 and tr_A0A2Y9M662_A0A2Y9M662_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C2S2_A0A2U4C2S2_TURTR_9739 and tr_A0A383ZKH3_A0A383ZKH3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3X1I0_A0A2U3X1I0_ODORO_9708 and tr_A0A2U3X4X7_A0A2U3X4X7_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2Y9DJR7_A0A2Y9DJR7_TRIMA_127582 and tr_A0A2Y9DK67_A0A2Y9DK67_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2Y9SY88_A0A2Y9SY88_PHYCD_9755 and tr_A0A2Y9T692_A0A2Y9T692_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 223 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/Q96QI5/3_mltree/Q96QI5.raxml.reduced.phy Alignment comprises 1 partitions and 189 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 189 / 189 Gaps: 1.09 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/3_mltree/Q96QI5.raxml.rba Parallelization scheme autoconfig: 4 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 189 / 15120 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -263126.361465] Initial branch length optimization [00:00:03 -207559.737072] Model parameter optimization (eps = 10.000000) [00:00:35 -206888.887935] AUTODETECT spr round 1 (radius: 5) [00:03:20 -137195.392921] AUTODETECT spr round 2 (radius: 10) [00:06:34 -101951.975925] AUTODETECT spr round 3 (radius: 15) [00:10:11 -80010.564500] AUTODETECT spr round 4 (radius: 20) [00:13:45 -72778.523809] AUTODETECT spr round 5 (radius: 25) [00:17:53 -68829.946109] SPR radius for FAST iterations: 25 (autodetect) [00:17:53 -68829.946109] Model parameter optimization (eps = 3.000000) [00:18:17 -68802.593831] FAST spr round 1 (radius: 25) [00:21:16 -57512.593446] FAST spr round 2 (radius: 25) [00:23:32 -56834.957412] FAST spr round 3 (radius: 25) [00:25:38 -56777.375702] FAST spr round 4 (radius: 25) [00:27:29 -56758.987592] FAST spr round 5 (radius: 25) [00:29:11 -56756.545965] FAST spr round 6 (radius: 25) [00:30:54 -56756.544794] Model parameter optimization (eps = 1.000000) [00:31:09 -56754.331970] SLOW spr round 1 (radius: 5) [00:33:29 -56737.030146] SLOW spr round 2 (radius: 5) [00:35:49 -56729.974424] SLOW spr round 3 (radius: 5) [00:38:05 -56729.627894] SLOW spr round 4 (radius: 5) [00:40:07 -56729.367452] SLOW spr round 5 (radius: 5) [00:41:59 -56729.367222] SLOW spr round 6 (radius: 10) [00:44:00 -56726.890825] SLOW spr round 7 (radius: 5) [00:46:47 -56724.880804] SLOW spr round 8 (radius: 5) [00:49:12 -56724.880770] SLOW spr round 9 (radius: 10) [00:51:28 -56724.813629] SLOW spr round 10 (radius: 15) [00:54:51 -56722.942517] SLOW spr round 11 (radius: 5) [00:57:41 -56722.942405] SLOW spr round 12 (radius: 10) [01:00:16 -56722.942404] SLOW spr round 13 (radius: 15) [01:03:29 -56722.942404] SLOW spr round 14 (radius: 20) [01:08:56 -56722.942404] SLOW spr round 15 (radius: 25) [01:15:29 -56722.942404] Model parameter optimization (eps = 0.100000) [01:15:38] [worker #0] ML tree search #1, logLikelihood: -56722.822078 [01:15:38 -265286.962854] Initial branch length optimization [01:15:42 -208911.136939] Model parameter optimization (eps = 10.000000) [01:16:25 -208225.869189] AUTODETECT spr round 1 (radius: 5) [01:19:14 -139147.743217] AUTODETECT spr round 2 (radius: 10) [01:22:26 -96715.769029] AUTODETECT spr round 3 (radius: 15) [01:25:33 -80637.810242] AUTODETECT spr round 4 (radius: 20) [01:28:54 -75438.245731] AUTODETECT spr round 5 (radius: 25) [01:31:42] [worker #1] ML tree search #2, logLikelihood: -56757.359356 [01:32:02] [worker #2] ML tree search #3, logLikelihood: -56726.766224 [01:32:50 -71341.907695] SPR radius for FAST iterations: 25 (autodetect) [01:32:50 -71341.907695] Model parameter optimization (eps = 3.000000) [01:33:14 -71290.988223] FAST spr round 1 (radius: 25) [01:36:27 -57767.294328] FAST spr round 2 (radius: 25) [01:38:47 -56936.262562] FAST spr round 3 (radius: 25) [01:40:46 -56777.339859] FAST spr round 4 (radius: 25) [01:42:39 -56765.145064] FAST spr round 5 (radius: 25) [01:44:22 -56765.144611] Model parameter optimization (eps = 1.000000) [01:44:40 -56758.646605] SLOW spr round 1 (radius: 5) [01:46:59 -56747.236152] SLOW spr round 2 (radius: 5) [01:49:12 -56739.921804] SLOW spr round 3 (radius: 5) [01:51:19 -56739.921720] SLOW spr round 4 (radius: 10) [01:53:34 -56733.014462] SLOW spr round 5 (radius: 5) [01:55:53] [worker #3] ML tree search #4, logLikelihood: -56726.794758 [01:56:14 -56732.418930] SLOW spr round 6 (radius: 5) [01:58:39 -56730.578004] SLOW spr round 7 (radius: 5) [02:00:52 -56730.577922] SLOW spr round 8 (radius: 10) [02:03:05 -56730.577916] SLOW spr round 9 (radius: 15) [02:06:27 -56730.577915] SLOW spr round 10 (radius: 20) [02:11:41 -56730.577914] SLOW spr round 11 (radius: 25) [02:18:04 -56730.577914] Model parameter optimization (eps = 0.100000) [02:18:11] [worker #0] ML tree search #5, logLikelihood: -56730.562259 [02:18:11 -262730.537625] Initial branch length optimization [02:18:15 -209212.592118] Model parameter optimization (eps = 10.000000) [02:19:09 -208546.786037] AUTODETECT spr round 1 (radius: 5) [02:21:59 -139544.829767] AUTODETECT spr round 2 (radius: 10) [02:25:12 -103588.831575] AUTODETECT spr round 3 (radius: 15) [02:28:20 -84627.575031] AUTODETECT spr round 4 (radius: 20) [02:32:01 -74611.832605] AUTODETECT spr round 5 (radius: 25) [02:35:59 -69137.469529] SPR radius for FAST iterations: 25 (autodetect) [02:35:59 -69137.469529] Model parameter optimization (eps = 3.000000) [02:36:21 -69116.610926] FAST spr round 1 (radius: 25) [02:39:29 -57761.991335] FAST spr round 2 (radius: 25) [02:40:06] [worker #2] ML tree search #7, logLikelihood: -56721.707733 [02:41:50 -56979.239022] FAST spr round 3 (radius: 25) [02:43:53 -56794.413401] FAST spr round 4 (radius: 25) [02:45:46 -56781.785824] FAST spr round 5 (radius: 25) [02:47:33 -56773.127819] FAST spr round 6 (radius: 25) [02:49:17 -56773.023396] FAST spr round 7 (radius: 25) [02:50:03] [worker #1] ML tree search #6, logLikelihood: -57468.844875 [02:50:59 -56773.005604] Model parameter optimization (eps = 1.000000) [02:51:18 -56770.137072] SLOW spr round 1 (radius: 5) [02:53:40 -56758.805164] SLOW spr round 2 (radius: 5) [02:55:52 -56756.902450] SLOW spr round 3 (radius: 5) [02:58:00 -56756.718538] SLOW spr round 4 (radius: 5) [03:00:08 -56756.718035] SLOW spr round 5 (radius: 10) [03:02:24 -56752.607346] SLOW spr round 6 (radius: 5) [03:05:12 -56751.908510] SLOW spr round 7 (radius: 5) [03:07:40 -56751.908451] SLOW spr round 8 (radius: 10) [03:10:02 -56748.458741] SLOW spr round 9 (radius: 5) [03:12:48 -56747.124500] SLOW spr round 10 (radius: 5) [03:15:14 -56747.123681] SLOW spr round 11 (radius: 10) [03:17:35 -56746.341160] SLOW spr round 12 (radius: 5) [03:20:20 -56746.341154] SLOW spr round 13 (radius: 10) [03:22:47 -56746.341125] SLOW spr round 14 (radius: 15) [03:26:05 -56746.341125] SLOW spr round 15 (radius: 20) [03:28:52] [worker #3] ML tree search #8, logLikelihood: -56755.558345 [03:31:24 -56746.341125] SLOW spr round 16 (radius: 25) [03:38:01 -56746.341125] Model parameter optimization (eps = 0.100000) [03:38:13] [worker #0] ML tree search #9, logLikelihood: -56746.059535 [03:38:13 -263859.291871] Initial branch length optimization [03:38:16 -209848.236319] Model parameter optimization (eps = 10.000000) [03:39:12 -209167.663009] AUTODETECT spr round 1 (radius: 5) [03:42:05 -141371.530603] AUTODETECT spr round 2 (radius: 10) [03:45:19 -100657.381801] AUTODETECT spr round 3 (radius: 15) [03:48:31 -83954.244241] AUTODETECT spr round 4 (radius: 20) [03:52:32 -75143.666217] AUTODETECT spr round 5 (radius: 25) [03:56:17 -69350.063313] SPR radius for FAST iterations: 25 (autodetect) [03:56:17 -69350.063313] Model parameter optimization (eps = 3.000000) [03:56:38 -69326.411302] FAST spr round 1 (radius: 25) [03:59:55 -58573.195357] FAST spr round 2 (radius: 25) [04:02:18 -56980.016908] FAST spr round 3 (radius: 25) [04:04:37 -56825.010543] FAST spr round 4 (radius: 25) [04:06:13] [worker #2] ML tree search #11, logLikelihood: -57042.156233 [04:06:41 -56771.887077] FAST spr round 5 (radius: 25) [04:08:27 -56767.507033] FAST spr round 6 (radius: 25) [04:10:10 -56767.506900] Model parameter optimization (eps = 1.000000) [04:10:22 -56762.246246] SLOW spr round 1 (radius: 5) [04:12:38 -56751.724359] SLOW spr round 2 (radius: 5) [04:14:52 -56746.836512] SLOW spr round 3 (radius: 5) [04:15:21] [worker #1] ML tree search #10, logLikelihood: -57112.367806 [04:17:06 -56746.833192] SLOW spr round 4 (radius: 10) [04:19:25 -56746.832850] SLOW spr round 5 (radius: 15) [04:22:45 -56746.378322] SLOW spr round 6 (radius: 5) [04:25:42 -56745.289055] SLOW spr round 7 (radius: 5) [04:28:15 -56741.243116] SLOW spr round 8 (radius: 5) [04:30:32 -56741.243043] SLOW spr round 9 (radius: 10) [04:32:47 -56741.243031] SLOW spr round 10 (radius: 15) [04:36:05 -56741.243031] SLOW spr round 11 (radius: 20) [04:41:12 -56741.243031] SLOW spr round 12 (radius: 25) [04:47:32 -56741.243031] Model parameter optimization (eps = 0.100000) [04:47:41] [worker #0] ML tree search #13, logLikelihood: -56741.116498 [04:47:41 -263814.781296] Initial branch length optimization [04:47:45 -210197.668358] Model parameter optimization (eps = 10.000000) [04:48:25 -209573.016456] AUTODETECT spr round 1 (radius: 5) [04:51:16 -140246.317703] AUTODETECT spr round 2 (radius: 10) [04:53:14] [worker #3] ML tree search #12, logLikelihood: -56738.770854 [04:54:30 -99113.594131] AUTODETECT spr round 3 (radius: 15) [04:57:49 -77613.138503] AUTODETECT spr round 4 (radius: 20) [05:01:17 -71947.893082] AUTODETECT spr round 5 (radius: 25) [05:05:34 -65719.691877] SPR radius for FAST iterations: 25 (autodetect) [05:05:34 -65719.691877] Model parameter optimization (eps = 3.000000) [05:06:05 -65702.044354] FAST spr round 1 (radius: 25) [05:09:11 -57326.297500] FAST spr round 2 (radius: 25) [05:11:28 -56816.704214] FAST spr round 3 (radius: 25) [05:13:30 -56761.169646] FAST spr round 4 (radius: 25) [05:15:21 -56754.852693] FAST spr round 5 (radius: 25) [05:17:03 -56754.852595] Model parameter optimization (eps = 1.000000) [05:17:18 -56753.166014] SLOW spr round 1 (radius: 5) [05:19:34 -56744.443176] SLOW spr round 2 (radius: 5) [05:21:50 -56741.547829] SLOW spr round 3 (radius: 5) [05:24:03 -56739.935142] SLOW spr round 4 (radius: 5) [05:25:52] [worker #1] ML tree search #14, logLikelihood: -56770.664102 [05:26:16 -56739.935043] SLOW spr round 5 (radius: 10) [05:28:34 -56739.935003] SLOW spr round 6 (radius: 15) [05:29:42] [worker #2] ML tree search #15, logLikelihood: -56727.922469 [05:31:59 -56737.889297] SLOW spr round 7 (radius: 5) [05:34:56 -56737.883164] SLOW spr round 8 (radius: 10) [05:37:36 -56737.883062] SLOW spr round 9 (radius: 15) [05:40:45 -56737.883061] SLOW spr round 10 (radius: 20) [05:46:05 -56737.883061] SLOW spr round 11 (radius: 25) [05:52:05 -56737.883061] Model parameter optimization (eps = 0.100000) [05:52:11] [worker #0] ML tree search #17, logLikelihood: -56737.857180 [06:00:09] [worker #3] ML tree search #16, logLikelihood: -56772.016534 [06:30:29] [worker #1] ML tree search #18, logLikelihood: -56729.603471 [06:41:58] [worker #2] ML tree search #19, logLikelihood: -56736.889007 [07:31:37] [worker #3] ML tree search #20, logLikelihood: -56719.043260 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.142727,0.234828) (0.284197,0.391854) (0.309075,0.794093) (0.264000,2.309415) 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: -56719.043260 AIC score: 117448.086520 / AICc score: 8161508.086520 / BIC score: 123947.789285 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=189). 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/Q96QI5/3_mltree/Q96QI5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/3_mltree/Q96QI5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/3_mltree/Q96QI5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96QI5/3_mltree/Q96QI5.raxml.log Analysis started: 04-Jul-2021 15:48:19 / finished: 04-Jul-2021 23:19:57 Elapsed time: 27097.934 seconds Consumed energy: 2075.888 Wh (= 10 km in an electric car, or 52 km with an e-scooter!)