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 17:24:18 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/2_msa/Q9HCS5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5 --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/Q9HCS5/2_msa/Q9HCS5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 290 sites WARNING: Sequences tr_B4R188_B4R188_DROSI_7240 and tr_Q9VFU8_Q9VFU8_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R188_B4R188_DROSI_7240 and tr_B4HFS6_B4HFS6_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5P4B4_A0A1D5P4B4_CHICK_9031 and tr_G1N4K0_G1N4K0_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5P7E3_A0A1D5P7E3_CHICK_9031 and tr_A0A091ILY4_A0A091ILY4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5P7E3_A0A1D5P7E3_CHICK_9031 and tr_A0A091VTI4_A0A091VTI4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5P7E3_A0A1D5P7E3_CHICK_9031 and tr_A0A091HQ06_A0A091HQ06_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_G1NB16_G1NB16_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_U3IYL9_U3IYL9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A091ILL9_A0A091ILL9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A091VLR5_A0A091VLR5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A087RBG3_A0A087RBG3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A091WYN4_A0A091WYN4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A091GJN4_A0A091GJN4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A2I0MWM1_A0A2I0MWM1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A091ICF8_A0A091ICF8_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5PTP6_A0A1D5PTP6_CHICK_9031 and tr_A0A1V4KFS4_A0A1V4KFS4_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1BWD5_E1BWD5_CHICK_9031 and tr_G1NH21_G1NH21_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BWD5_E1BWD5_CHICK_9031 and tr_U3J462_U3J462_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q6P5H6_FRMD5_MOUSE_10090 and tr_F1LT14_F1LT14_RAT_10116 are exactly identical! WARNING: Sequences sp_Q6P5H6_FRMD5_MOUSE_10090 and tr_I3M8Y9_I3M8Y9_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q6P5H6_FRMD5_MOUSE_10090 and tr_A0A1S3EM92_A0A1S3EM92_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q6P5H6_FRMD5_MOUSE_10090 and tr_A0A3Q0CPL7_A0A3Q0CPL7_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_M3XPG9_M3XPG9_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_G1SV20_G1SV20_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_F1PAI1_F1PAI1_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and sp_Q9MYU8_E41L5_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_W5PTM7_W5PTM7_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_G1LPZ6_G1LPZ6_AILME_9646 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and sp_Q58CU2_E41L5_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_A0A337SFP6_A0A337SFP6_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_A0A1U7TV26_A0A1U7TV26_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_A0A2U3W942_A0A2U3W942_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_A0A2U3XY91_A0A2U3XY91_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q8BGS1_E41L5_MOUSE_10090 and tr_A0A384BP30_A0A384BP30_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_M3Y0U1_M3Y0U1_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_E2RHR4_E2RHR4_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_Q9JMB3_Q9JMB3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A2I2URV6_A0A2I2URV6_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A1S2ZIK9_A0A1S2ZIK9_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A2U3ZT57_A0A2U3ZT57_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A2U3Y3R9_A0A2U3Y3R9_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A2Y9J0B9_A0A2Y9J0B9_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q9WV92_E41L3_MOUSE_10090 and tr_A0A384C0N4_A0A384C0N4_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_M3Z258_M3Z258_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2I3GD50_A0A2I3GD50_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G1PJH0_G1PJH0_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G3SFI6_G3SFI6_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_H2P1T2_H2P1T2_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G1SL22_G1SL22_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2I3RMK9_A0A2I3RMK9_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_F6QNK6_F6QNK6_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_W5Q1K6_W5Q1K6_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_I3MXC7_I3MXC7_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_H0WJ71_H0WJ71_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and sp_Q9H4G0_E41L1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_F6UAX5_F6UAX5_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G5B840_G5B840_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G3SYG8_G3SYG8_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2R8MGF6_A0A2R8MGF6_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A287AVU3_A0A287AVU3_PIG_9823 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_G1LU01_G1LU01_AILME_9646 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_F1N611_F1N611_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_L5JYJ9_L5JYJ9_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2I2UI66_A0A2I2UI66_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2I3M5V1_A0A2I3M5V1_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A0D9RCE7_A0A0D9RCE7_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A3Q0DIL6_A0A3Q0DIL6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2K5NGU0_A0A2K5NGU0_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2K6A326_A0A2K6A326_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2R9AYJ0_A0A2R9AYJ0_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2U3VEU9_A0A2U3VEU9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2U3YFV3_A0A2U3YFV3_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2Y9QC34_A0A2Y9QC34_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2Y9IQN2_A0A2Y9IQN2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2Y9PMT5_A0A2Y9PMT5_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A2Y9T614_A0A2Y9T614_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A384CNE7_A0A384CNE7_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q9Z2H5_E41L1_MOUSE_10090 and tr_A0A384B103_A0A384B103_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_F1P7P5_F1P7P5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_G5BM59_G5BM59_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_F1MGE1_F1MGE1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_L5K2C2_L5K2C2_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_A0A337SMB0_A0A337SMB0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_A0A1S3AFI9_A0A1S3AFI9_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_A0A2U3ZRV3_A0A2U3ZRV3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_A0A2U3X7Q5_A0A2U3X7Q5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YGW4_M3YGW4_MUSPF_9669 and tr_A0A2Y9SEC4_A0A2Y9SEC4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YT76_M3YT76_MUSPF_9669 and tr_G1LMG3_G1LMG3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YT76_M3YT76_MUSPF_9669 and tr_A0A2Y9JDY5_A0A2Y9JDY5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YT76_M3YT76_MUSPF_9669 and tr_A0A384C3A0_A0A384C3A0_URSMA_29073 are exactly identical! WARNING: Sequences tr_B4JI80_B4JI80_DROGR_7222 and tr_B4M6A5_B4M6A5_DROVI_7244 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_G3RLI5_G3RLI5_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_H2Q9B7_H2Q9B7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_B5SNK2_B5SNK2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and sp_Q7Z6J6_FRMD5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_F7G8P4_F7G8P4_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_U3E038_U3E038_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_G7PB80_G7PB80_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A2I3M9B9_A0A2I3M9B9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A0D9RAY5_A0A0D9RAY5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A2K5MLF7_A0A2K5MLF7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A2K6BDC5_A0A2K6BDC5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A2K5XD94_A0A2K5XD94_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A2R9AYL7_A0A2R9AYL7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3H9H7_A0A2I3H9H7_NOMLE_61853 and tr_A0A384B8P9_A0A384B8P9_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_G3SF44_G3SF44_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_H2QE82_H2QE82_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and sp_Q9Y2J2_E41L3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_G7NKD7_G7NKD7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_U3FRC1_U3FRC1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_G7PWE9_G7PWE9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A2I3MPL2_A0A2I3MPL2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A0D9RYC3_A0A0D9RYC3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A2K5MF59_A0A2K5MF59_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A2K6DME0_A0A2K6DME0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A2K6ACJ9_A0A2K6ACJ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R5G2_G1R5G2_NOMLE_61853 and tr_A0A2R9AJB0_A0A2R9AJB0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_G3QNK1_G3QNK1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_H2PT00_H2PT00_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_H2QXN9_H2QXN9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and sp_Q9H329_E41LB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_F6UVV7_F6UVV7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_G7PRQ3_G7PRQ3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S6L5_G1S6L5_NOMLE_61853 and tr_A0A2R8ZY52_A0A2R8ZY52_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YW63_A0A2I2YW63_GORGO_9595 and sp_Q9HCM4_E41L5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YW63_A0A2I2YW63_GORGO_9595 and tr_A0A1D5QMD8_A0A1D5QMD8_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YW63_A0A2I2YW63_GORGO_9595 and tr_A0A0D9RVR2_A0A0D9RVR2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2YW63_A0A2I2YW63_GORGO_9595 and tr_A0A2K5NAF6_A0A2K5NAF6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2YW63_A0A2I2YW63_GORGO_9595 and tr_A0A2K6BU75_A0A2K6BU75_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QKS3_G3QKS3_GORGO_9595 and tr_H2QIM7_H2QIM7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_H2PKB6_H2PKB6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_H2QTQ8_H2QTQ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and sp_O43491_E41L2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_A0A2R9A1P9_A0A2R9A1P9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_A0A2J8JCK6_A0A2J8JCK6_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and sp_P11171_41_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_F6WEM9_F6WEM9_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_G8F3Y8_G8F3Y8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_A0A2K5LAS1_A0A2K5LAS1_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_A0A2K5XLL1_A0A2K5XLL1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2N894_H2N894_PONAB_9601 and tr_A0A2R9BLM6_A0A2R9BLM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0R3NF20_A0A0R3NF20_DROPS_46245 and tr_B4GYS9_B4GYS9_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q297Q7_Q297Q7_DROPS_46245 and tr_B4G2W2_B4G2W2_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1Q1Y8_F1Q1Y8_CANLF_9615 and tr_A0A2I2UPW9_A0A2I2UPW9_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3RAU7_A0A2I3RAU7_PANTR_9598 and tr_A0A2R9BIL3_A0A2R9BIL3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QRB4_H2QRB4_PANTR_9598 and tr_A0A2R9C1I3_A0A2R9C1I3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7EL54_F7EL54_MONDO_13616 and tr_G3WPV6_G3WPV6_SARHA_9305 are exactly identical! WARNING: Sequences tr_F7GDV6_F7GDV6_MONDO_13616 and tr_G3VZ11_G3VZ11_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5NX11_W5NX11_SHEEP_9940 and sp_Q9N179_41_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5QQA1_A0A3B5QQA1_XIPMA_8083 and tr_A0A087X3G5_A0A087X3G5_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4ARM9_M4ARM9_XIPMA_8083 and tr_A0A087YE41_A0A087YE41_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZX48_A0A087ZX48_APIME_7460 and tr_A0A2A3EDG3_A0A2A3EDG3_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A088AHP6_A0A088AHP6_APIME_7460 and tr_A0A2A3E4U4_A0A2A3E4U4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NJY3_A0A158NJY3_ATTCE_12957 and tr_F4WIK9_F4WIK9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NWC3_A0A158NWC3_ATTCE_12957 and tr_F4X4T4_F4X4T4_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NWC3_A0A158NWC3_ATTCE_12957 and tr_A0A151X4Z2_A0A151X4Z2_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NWC3_A0A158NWC3_ATTCE_12957 and tr_A0A151HYL1_A0A151HYL1_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NWC3_A0A158NWC3_ATTCE_12957 and tr_A0A195ESD3_A0A195ESD3_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NWC3_A0A158NWC3_ATTCE_12957 and tr_A0A151IC14_A0A151IC14_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A0K0JJB4_A0A0K0JJB4_BRUMA_6279 and tr_A0A158PRD3_A0A158PRD3_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0JJB4_A0A0K0JJB4_BRUMA_6279 and tr_A0A0R3Q3L7_A0A0R3Q3L7_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A1D5R3E9_A0A1D5R3E9_MACMU_9544 and tr_G7P821_G7P821_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R3E9_A0A1D5R3E9_MACMU_9544 and tr_A0A2K6CA35_A0A2K6CA35_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_G7PN58_G7PN58_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A096MX43_A0A096MX43_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A0D9RVP8_A0A0D9RVP8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K6CIJ0_A0A2K6CIJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K5ZW56_A0A2K5ZW56_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BWK5_F7BWK5_MACMU_9544 and tr_G7P362_G7P362_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BWK5_F7BWK5_MACMU_9544 and tr_A0A0D9RVP3_A0A0D9RVP3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BWK5_F7BWK5_MACMU_9544 and tr_A0A2K5NP78_A0A2K5NP78_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BWK5_F7BWK5_MACMU_9544 and tr_A0A2K5ZFZ3_A0A2K5ZFZ3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5B4R3_G5B4R3_HETGA_10181 and tr_A0A2Y9KPW0_A0A2Y9KPW0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_Q7QB86_Q7QB86_ANOGA_7165 and tr_A0A084VLA8_A0A084VLA8_ANOSI_74873 are exactly identical! WARNING: Sequences tr_H0YYC9_H0YYC9_TAEGU_59729 and tr_A0A218V9Z3_A0A218V9Z3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZCP2_H0ZCP2_TAEGU_59729 and tr_U3JPE9_U3JPE9_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZCP2_H0ZCP2_TAEGU_59729 and tr_A0A218VBN0_A0A218VBN0_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZIA9_H0ZIA9_TAEGU_59729 and tr_A0A093QDW2_A0A093QDW2_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZIA9_H0ZIA9_TAEGU_59729 and tr_A0A093G6U5_A0A093G6U5_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZIA9_H0ZIA9_TAEGU_59729 and tr_A0A218UUA3_A0A218UUA3_9PASE_299123 are exactly identical! WARNING: Sequences tr_E3NGZ5_E3NGZ5_CAERE_31234 and tr_A0A261BFP2_A0A261BFP2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8X7Z5_A8X7Z5_CAEBR_6238 and tr_A0A2G5USK9_A0A2G5USK9_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G1LY98_G1LY98_AILME_9646 and tr_A0A384CE91_A0A384CE91_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1MD05_F1MD05_BOVIN_9913 and tr_A0A1S3FS51_A0A1S3FS51_DIPOR_10020 are exactly identical! WARNING: Sequences tr_F1MD05_F1MD05_BOVIN_9913 and tr_A0A2Y9NLA4_A0A2Y9NLA4_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1MD05_F1MD05_BOVIN_9913 and tr_A0A2Y9SZS2_A0A2Y9SZS2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3W969_M3W969_FELCA_9685 and tr_A0A2Y9JJ76_A0A2Y9JJ76_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3KAZ6_U3KAZ6_FICAL_59894 and tr_A0A091VVY7_A0A091VVY7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3KE75_U3KE75_FICAL_59894 and tr_A0A091EA88_A0A091EA88_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KE75_U3KE75_FICAL_59894 and tr_A0A218U9K9_A0A218U9K9_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A151NEQ2_A0A151NEQ2_ALLMI_8496 and tr_A0A093H678_A0A093H678_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A151NEQ2_A0A151NEQ2_ALLMI_8496 and tr_A0A0A0A3G3_A0A0A0A3G3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A151NZB5_A0A151NZB5_ALLMI_8496 and tr_A0A1U7S345_A0A1U7S345_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PG76_A0A151PG76_ALLMI_8496 and tr_A0A3Q0GE57_A0A3Q0GE57_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3TVM0_A0A0Q3TVM0_AMAAE_12930 and tr_A0A1V4JDL5_A0A1V4JDL5_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0Q3TVM0_A0A0Q3TVM0_AMAAE_12930 and tr_A0A218UEI7_A0A218UEI7_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0Q3TVM0_A0A0Q3TVM0_AMAAE_12930 and tr_A0A226N5E6_A0A226N5E6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A0Q3TVM0_A0A0Q3TVM0_AMAAE_12930 and tr_A0A226PCE9_A0A226PCE9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A091F1H9_A0A091F1H9_CORBR_85066 and tr_A0A093PTT4_A0A093PTT4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JIF4_A0A091JIF4_EGRGA_188379 and tr_A0A091VF77_A0A091VF77_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A194R1F3_A0A194R1F3_PAPMA_76193 and tr_A0A194PX51_A0A194PX51_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A093QLG2_A0A093QLG2_9PASS_328815 and tr_A0A1V4J8Q7_A0A1V4J8Q7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A087R3U9_A0A087R3U9_APTFO_9233 and tr_A0A0A0AKQ9_A0A0A0AKQ9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LNT3_A0A2I0LNT3_COLLI_8932 and tr_A0A1V4JEV0_A0A1V4JEV0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MGL0_A0A2I0MGL0_COLLI_8932 and tr_A0A1V4K636_A0A1V4K636_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V0W710_A0A0V0W710_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V0V180_A0A0V0V180_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V1KV56_A0A0V1KV56_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V1A9K5_A0A0V1A9K5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V1PJP1_A0A0V1PJP1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V0UE85_A0A0V0UE85_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1N7X8_A0A0V1N7X8_9BILA_268474 and tr_A0A0V1HYG4_A0A0V1HYG4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3K4Y6_A0A1S3K4Y6_LINUN_7574 and tr_A0A1S3K5J1_A0A1S3K5J1_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3LT66_A0A1S3LT66_SALSA_8030 and tr_C0H8W7_C0H8W7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3MLT2_A0A1S3MLT2_SALSA_8030 and tr_A0A060WUX2_A0A060WUX2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PMJ0_A0A1S3PMJ0_SALSA_8030 and tr_C0H9D5_C0H9D5_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RYX8_A0A1S3RYX8_SALSA_8030 and tr_A0A1S3RZA5_A0A1S3RZA5_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1D1VLU4_A0A1D1VLU4_RAMVA_947166 and tr_A0A1D1VUC7_A0A1D1VUC7_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2D0Q8M8_A0A2D0Q8M8_ICTPU_7998 and tr_A0A2D0QB94_A0A2D0QB94_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R2D4_A0A2D0R2D4_ICTPU_7998 and tr_W5UFK7_W5UFK7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R2I7_A0A2D0R2I7_ICTPU_7998 and tr_A0A2D0R404_A0A2D0R404_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SS53_A0A2D0SS53_ICTPU_7998 and tr_W5UL47_W5UL47_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KI90_A0A2K5KI90_CERAT_9531 and tr_A0A2K5Y517_A0A2K5Y517_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4B3T0_A0A2U4B3T0_TURTR_9739 and tr_A0A2U4B3U7_A0A2U4B3U7_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4B3T0_A0A2U4B3T0_TURTR_9739 and tr_A0A2U4B3Y6_A0A2U4B3Y6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4B3T0_A0A2U4B3T0_TURTR_9739 and tr_A0A2U4B482_A0A2U4B482_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BKU0_A0A2U4BKU0_TURTR_9739 and tr_A0A2Y9LG36_A0A2Y9LG36_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VPJ5_A0A2U3VPJ5_ODORO_9708 and tr_A0A2U3XX21_A0A2U3XX21_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 228 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/Q9HCS5/3_mltree/Q9HCS5.raxml.reduced.phy Alignment comprises 1 partitions and 290 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 290 / 290 Gaps: 1.05 % Invariant sites: 0.34 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5.raxml.rba Parallelization scheme autoconfig: 6 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 / 290 / 23200 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -445083.851317] Initial branch length optimization [00:00:07 -361856.105281] Model parameter optimization (eps = 10.000000) [00:01:12 -361065.047343] AUTODETECT spr round 1 (radius: 5) [00:04:59 -189441.731046] AUTODETECT spr round 2 (radius: 10) [00:08:30 -129169.997797] AUTODETECT spr round 3 (radius: 15) [00:12:21 -104923.178643] AUTODETECT spr round 4 (radius: 20) [00:16:49 -92959.153040] AUTODETECT spr round 5 (radius: 25) [00:21:53 -86385.945660] SPR radius for FAST iterations: 25 (autodetect) [00:21:53 -86385.945660] Model parameter optimization (eps = 3.000000) [00:22:20 -86274.852822] FAST spr round 1 (radius: 25) [00:25:50 -67793.981350] FAST spr round 2 (radius: 25) [00:28:36 -62729.874593] FAST spr round 3 (radius: 25) [00:30:57 -61664.089793] FAST spr round 4 (radius: 25) [00:33:13 -61594.380004] FAST spr round 5 (radius: 25) [00:35:18 -61592.550899] FAST spr round 6 (radius: 25) [00:37:13 -61592.550874] Model parameter optimization (eps = 1.000000) [00:37:29 -61589.099835] SLOW spr round 1 (radius: 5) [00:40:12 -61576.331005] SLOW spr round 2 (radius: 5) [00:42:52 -61574.891305] SLOW spr round 3 (radius: 5) [00:45:23 -61574.890929] SLOW spr round 4 (radius: 10) [00:48:02 -61574.168320] SLOW spr round 5 (radius: 5) [00:51:19 -61573.669239] SLOW spr round 6 (radius: 5) [00:54:12 -61573.669232] SLOW spr round 7 (radius: 10) [00:56:59 -61573.669226] SLOW spr round 8 (radius: 15) [01:01:01 -61573.308405] SLOW spr round 9 (radius: 5) [01:04:31 -61573.308398] SLOW spr round 10 (radius: 10) [01:07:47 -61573.308392] SLOW spr round 11 (radius: 15) [01:11:41 -61573.308391] SLOW spr round 12 (radius: 20) [01:18:07 -61573.308391] SLOW spr round 13 (radius: 25) [01:24:52] [worker #1] ML tree search #2, logLikelihood: -61565.858737 [01:27:36 -61573.308390] Model parameter optimization (eps = 0.100000) [01:27:49] [worker #0] ML tree search #1, logLikelihood: -61571.719026 [01:27:49 -444697.531345] Initial branch length optimization [01:27:51] [worker #2] ML tree search #3, logLikelihood: -61578.881036 [01:27:58 -360610.476015] Model parameter optimization (eps = 10.000000) [01:29:03 -359908.904752] AUTODETECT spr round 1 (radius: 5) [01:30:40] [worker #4] ML tree search #5, logLikelihood: -61565.783542 [01:30:46] [worker #5] ML tree search #6, logLikelihood: -61569.610300 [01:32:54 -184898.995589] AUTODETECT spr round 2 (radius: 10) [01:36:23 -121836.790617] AUTODETECT spr round 3 (radius: 15) [01:40:06 -98415.620391] AUTODETECT spr round 4 (radius: 20) [01:44:19 -82086.921362] AUTODETECT spr round 5 (radius: 25) [01:44:56] [worker #3] ML tree search #4, logLikelihood: -61567.023484 [01:49:45 -78187.798586] SPR radius for FAST iterations: 25 (autodetect) [01:49:45 -78187.798586] Model parameter optimization (eps = 3.000000) [01:50:11 -78088.000533] FAST spr round 1 (radius: 25) [01:53:35 -63819.253080] FAST spr round 2 (radius: 25) [01:56:17 -61787.391555] FAST spr round 3 (radius: 25) [01:58:38 -61612.723667] FAST spr round 4 (radius: 25) [02:00:41 -61605.436340] FAST spr round 5 (radius: 25) [02:02:37 -61605.436328] Model parameter optimization (eps = 1.000000) [02:02:52 -61602.620798] SLOW spr round 1 (radius: 5) [02:05:32 -61583.747793] SLOW spr round 2 (radius: 5) [02:08:11 -61579.158114] SLOW spr round 3 (radius: 5) [02:10:51 -61579.157425] SLOW spr round 4 (radius: 10) [02:13:37 -61578.136084] SLOW spr round 5 (radius: 5) [02:17:00 -61578.135968] SLOW spr round 6 (radius: 10) [02:20:03 -61578.135927] SLOW spr round 7 (radius: 15) [02:24:02 -61578.131954] SLOW spr round 8 (radius: 20) [02:30:07 -61578.131954] SLOW spr round 9 (radius: 25) [02:37:52] [worker #1] ML tree search #8, logLikelihood: -61561.354665 [02:38:51 -61578.131954] Model parameter optimization (eps = 0.100000) [02:38:57] [worker #0] ML tree search #7, logLikelihood: -61578.070692 [02:38:57 -442330.845992] Initial branch length optimization [02:39:03 -359790.619208] Model parameter optimization (eps = 10.000000) [02:39:55 -359110.651434] AUTODETECT spr round 1 (radius: 5) [02:43:44 -193505.707042] AUTODETECT spr round 2 (radius: 10) [02:47:17 -125223.123057] AUTODETECT spr round 3 (radius: 15) [02:48:11] [worker #5] ML tree search #12, logLikelihood: -61575.452897 [02:51:01 -101760.516442] AUTODETECT spr round 4 (radius: 20) [02:55:30 -88137.814845] AUTODETECT spr round 5 (radius: 25) [02:56:09] [worker #3] ML tree search #10, logLikelihood: -61562.510149 [02:57:01] [worker #4] ML tree search #11, logLikelihood: -61581.544333 [03:01:55 -76452.616320] SPR radius for FAST iterations: 25 (autodetect) [03:01:55 -76452.616320] Model parameter optimization (eps = 3.000000) [03:02:28 -76336.650462] FAST spr round 1 (radius: 25) [03:03:36] [worker #2] ML tree search #9, logLikelihood: -61571.221095 [03:05:43 -63237.862860] FAST spr round 2 (radius: 25) [03:08:21 -61894.785127] FAST spr round 3 (radius: 25) [03:10:36 -61601.813975] FAST spr round 4 (radius: 25) [03:12:44 -61596.347159] FAST spr round 5 (radius: 25) [03:14:42 -61596.174767] FAST spr round 6 (radius: 25) [03:16:39 -61595.701808] FAST spr round 7 (radius: 25) [03:18:34 -61595.701791] Model parameter optimization (eps = 1.000000) [03:18:43 -61594.801667] SLOW spr round 1 (radius: 5) [03:21:21 -61577.190377] SLOW spr round 2 (radius: 5) [03:24:02 -61577.188702] SLOW spr round 3 (radius: 10) [03:26:49 -61577.188276] SLOW spr round 4 (radius: 15) [03:31:06 -61577.187731] SLOW spr round 5 (radius: 20) [03:37:18 -61576.826408] SLOW spr round 6 (radius: 5) [03:41:03 -61576.826145] SLOW spr round 7 (radius: 10) [03:44:26 -61576.826109] SLOW spr round 8 (radius: 15) [03:48:21 -61576.826109] SLOW spr round 9 (radius: 20) [03:54:36 -61576.826109] SLOW spr round 10 (radius: 25) [04:03:53 -61576.826109] Model parameter optimization (eps = 0.100000) [04:03:59] [worker #0] ML tree search #13, logLikelihood: -61576.810048 [04:04:00 -442888.575505] Initial branch length optimization [04:04:06 -362180.972889] Model parameter optimization (eps = 10.000000) [04:05:03 -361448.935030] AUTODETECT spr round 1 (radius: 5) [04:05:37] [worker #4] ML tree search #17, logLikelihood: -61571.485204 [04:06:57] [worker #5] ML tree search #18, logLikelihood: -61578.372695 [04:08:56 -193770.433148] AUTODETECT spr round 2 (radius: 10) [04:12:30 -124431.091853] AUTODETECT spr round 3 (radius: 15) [04:16:14 -104750.736398] AUTODETECT spr round 4 (radius: 20) [04:20:30 -91043.895483] AUTODETECT spr round 5 (radius: 25) [04:20:52] [worker #3] ML tree search #16, logLikelihood: -61588.111440 [04:20:55] [worker #2] ML tree search #15, logLikelihood: -61571.350693 [04:25:34 -77802.163744] SPR radius for FAST iterations: 25 (autodetect) [04:25:34 -77802.163744] Model parameter optimization (eps = 3.000000) [04:25:59 -77712.547250] FAST spr round 1 (radius: 25) [04:29:31 -62971.674546] FAST spr round 2 (radius: 25) [04:32:12 -61835.015537] FAST spr round 3 (radius: 25) [04:34:31 -61634.552469] FAST spr round 4 (radius: 25) [04:36:47 -61598.829742] FAST spr round 5 (radius: 25) [04:38:48 -61591.589198] FAST spr round 6 (radius: 25) [04:40:45 -61588.816808] FAST spr round 7 (radius: 25) [04:42:40 -61588.816776] Model parameter optimization (eps = 1.000000) [04:42:49 -61587.957154] SLOW spr round 1 (radius: 5) [04:43:25] [worker #1] ML tree search #14, logLikelihood: -61573.872013 [04:45:31 -61568.418518] SLOW spr round 2 (radius: 5) [04:48:13 -61567.719091] SLOW spr round 3 (radius: 5) [04:50:53 -61567.718783] SLOW spr round 4 (radius: 10) [04:53:40 -61566.948778] SLOW spr round 5 (radius: 5) [04:57:05 -61566.948706] SLOW spr round 6 (radius: 10) [05:00:14 -61566.948649] SLOW spr round 7 (radius: 15) [05:04:16 -61566.948631] SLOW spr round 8 (radius: 20) [05:10:37 -61566.948630] SLOW spr round 9 (radius: 25) [05:19:39 -61566.948629] Model parameter optimization (eps = 0.100000) [05:19:50] [worker #0] ML tree search #19, logLikelihood: -61566.732549 [06:06:42] [worker #1] ML tree search #20, logLikelihood: -61561.782511 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.203335,0.374840) (0.255138,0.557033) (0.353867,1.013428) (0.187660,2.254302) 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: -61561.354665 AIC score: 127132.709329 / AICc score: 8171192.709329 / BIC score: 134490.820580 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=290). 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/Q9HCS5/3_mltree/Q9HCS5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5.raxml.log Analysis started: 04-Jul-2021 17:24:18 / finished: 04-Jul-2021 23:31:00 Elapsed time: 22002.340 seconds Consumed energy: 1759.344 Wh (= 9 km in an electric car, or 44 km with an e-scooter!)