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 03-Jul-2021 18:46:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/2_msa/Q8N1P7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/2_msa/Q8N1P7_trimmed_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 121 sites WARNING: Sequences sp_P55165_CRBB3_CHICK_9031 and tr_G3UU63_G3UU63_MELGA_9103 are exactly identical! WARNING: Sequences sp_P55165_CRBB3_CHICK_9031 and tr_A0A226MV10_A0A226MV10_CALSU_9009 are exactly identical! WARNING: Sequences sp_P55165_CRBB3_CHICK_9031 and tr_A0A226PY36_A0A226PY36_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A0G2JG52_A0A0G2JG52_MOUSE_10090 and tr_D3ZD79_D3ZD79_RAT_10116 are exactly identical! WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and sp_P62697_CRBB2_RAT_10116 are exactly identical! WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and tr_A0A1U7Q218_A0A1U7Q218_MESAU_10036 are exactly identical! WARNING: Sequences sp_P62696_CRBB2_MOUSE_10090 and sp_P62698_CRBB2_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9JJU9_CRBB3_MOUSE_10090 and tr_G3HVI7_G3HVI7_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q9JJU9_CRBB3_MOUSE_10090 and sp_P02524_CRBB3_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XU37_M3XU37_MUSPF_9669 and tr_D2HDJ4_D2HDJ4_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XU37_M3XU37_MUSPF_9669 and tr_A0A2U3VB78_A0A2U3VB78_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XU37_M3XU37_MUSPF_9669 and tr_A0A384BZ91_A0A384BZ91_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YC57_M3YC57_MUSPF_9669 and tr_A0A2Y9K901_A0A2Y9K901_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YDQ9_M3YDQ9_MUSPF_9669 and tr_A0A2Y9KPM7_A0A2Y9KPM7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQ86_M3YQ86_MUSPF_9669 and tr_A0A2Y9KWZ3_A0A2Y9KWZ3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQF1_M3YQF1_MUSPF_9669 and sp_Q2LEC2_CRBB2_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YQF1_M3YQF1_MUSPF_9669 and tr_M3WJG9_M3WJG9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YQF1_M3YQF1_MUSPF_9669 and tr_A0A2Y9KXS2_A0A2Y9KXS2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQH0_M3YQH0_MUSPF_9669 and tr_F2Z4Y7_F2Z4Y7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YQH0_M3YQH0_MUSPF_9669 and tr_A0A337S730_A0A337S730_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YQH0_M3YQH0_MUSPF_9669 and tr_A0A2U3XPC3_A0A2U3XPC3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_G3S9C7_G3S9C7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_H2RHK4_H2RHK4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and sp_Q68DQ2_CRBG3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_G7NZ69_G7NZ69_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A096NWE1_A0A096NWE1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A0D9R0Y6_A0A0D9R0Y6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A2K5LVH0_A0A2K5LVH0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A2K6E1R4_A0A2K6E1R4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A2K5XHA7_A0A2K5XHA7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QNB6_G1QNB6_NOMLE_61853 and tr_A0A2R9BY08_A0A2R9BY08_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_H2P3W0_H2P3W0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and sp_A2IBH5_CRBB2_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_I3M1E5_I3M1E5_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A4L9L6_A4L9L6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and sp_P43320_CRBB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_F7IAH0_F7IAH0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A096NW62_A0A096NW62_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A0D9RCT3_A0A0D9RCT3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R850_G1R850_NOMLE_61853 and tr_A0A2K5NA26_A0A2K5NA26_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and tr_G3QXJ2_G3QXJ2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and tr_H2N8F9_H2N8F9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and tr_A0A2I3STH5_A0A2I3STH5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and sp_Q8N1P7_CRBG2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and tr_A0A0D9S847_A0A0D9S847_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RDL4_G1RDL4_NOMLE_61853 and tr_A0A2K5M5A0_A0A2K5M5A0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3HTC3_G3HTC3_CRIGR_10029 and tr_A0A1U8CHR0_A0A1U8CHR0_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3I3D3_G3I3D3_CRIGR_10029 and tr_A0A1U7QUU8_A0A1U7QUU8_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3RCE9_G3RCE9_GORGO_9595 and sp_P22914_CRYGS_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RCS4_G3RCS4_GORGO_9595 and sp_P53674_CRBB1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and tr_H2QJB0_H2QJB0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and sp_P07320_CRGD_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_H2P8F7_H2P8F7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_H2QJB1_H2QJB1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and sp_P07315_CRGC_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and sp_A3RLD8_CRGC_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_G7PLA8_G7PLA8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A0D9RCG4_A0A0D9RCG4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A2K5MJV9_A0A2K5MJV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A2K6B305_A0A2K6B305_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A2K6AKB7_A0A2K6AKB7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_A0A2R9A6L2_A0A2R9A6L2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SGF7_G3SGF7_GORGO_9595 and tr_H2R0F6_H2R0F6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGF7_G3SGF7_GORGO_9595 and tr_A0A2R9A076_A0A2R9A076_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PJY0_H2PJY0_PONAB_9601 and tr_H2QTH3_H2QTH3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PJY0_H2PJY0_PONAB_9601 and sp_Q9Y4K1_CRBG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PJY0_H2PJY0_PONAB_9601 and tr_A0A2R9AHZ4_A0A2R9AHZ4_PANPA_9597 are exactly identical! WARNING: Sequences sp_A2IBY7_CRYGS_CANLF_9615 and tr_G1L2Q3_G1L2Q3_AILME_9646 are exactly identical! WARNING: Sequences sp_A2IBY7_CRYGS_CANLF_9615 and tr_A0A2U3WVG0_A0A2U3WVG0_ODORO_9708 are exactly identical! WARNING: Sequences sp_A2IBY7_CRYGS_CANLF_9615 and tr_A0A2U3YHV0_A0A2U3YHV0_LEPWE_9713 are exactly identical! WARNING: Sequences sp_A2IBY7_CRYGS_CANLF_9615 and tr_A0A384D8Z6_A0A384D8Z6_URSMA_29073 are exactly identical! WARNING: Sequences tr_E2R7P2_E2R7P2_CANLF_9615 and tr_L5L5A4_L5L5A4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F1PFQ4_F1PFQ4_CANLF_9615 and tr_M3W3G3_M3W3G3_FELCA_9685 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and sp_P11844_CRGA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and tr_A7KK28_A7KK28_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QLE9_H2QLE9_PANTR_9598 and tr_A0A2R9A3H6_A0A2R9A3H6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RCF8_H2RCF8_PANTR_9598 and tr_A0A2R9CI67_A0A2R9CI67_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7F7L0_F7F7L0_MONDO_13616 and tr_G3VWI7_G3VWI7_SARHA_9305 are exactly identical! WARNING: Sequences tr_Q52NW3_Q52NW3_SHEEP_9940 and sp_P19141_CRBB3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5NUB1_W5NUB1_SHEEP_9940 and sp_P11842_CRBA4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QCG5_W5QCG5_SHEEP_9940 and sp_P02522_CRBB2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H0X6A9_H0X6A9_OTOGA_30611 and tr_I3LUY9_I3LUY9_PIG_9823 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_G7PLA9_G7PLA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2I3N8B8_A0A2I3N8B8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A0D9RCE9_A0A0D9RCE9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K5NYX4_A0A2K5NYX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K6DKZ9_A0A2K6DKZ9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K6A4K3_A0A2K6A4K3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6PWY4_F6PWY4_MACMU_9544 and tr_A0A2I3MKU1_A0A2I3MKU1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6PWY4_F6PWY4_MACMU_9544 and tr_A0A2K5MMW1_A0A2K5MMW1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QMR1_F6QMR1_MACMU_9544 and tr_A0A2K6C8B5_A0A2K6C8B5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QMR1_F6QMR1_MACMU_9544 and tr_A0A2K5XJF1_A0A2K5XJF1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_G7NYM3_G7NYM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A096NCK3_A0A096NCK3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A0D9RNN2_A0A0D9RNN2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5P3E0_A0A2K5P3E0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K6C2J9_A0A2K6C2J9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5XZH8_A0A2K5XZH8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_G7PLA7_G7PLA7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2I3MTV9_A0A2I3MTV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A0D9RCG7_A0A0D9RCG7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5MVY4_A0A2K5MVY4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5XTU2_A0A2K5XTU2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7F0F8_F7F0F8_MACMU_9544 and tr_G7PHG1_G7PHG1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F0F8_F7F0F8_MACMU_9544 and tr_A0A0D9RCD2_A0A0D9RCD2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7F0F8_F7F0F8_MACMU_9544 and tr_A0A2K6CA33_A0A2K6CA33_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_G7PHG2_G7PHG2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A096NRG8_A0A096NRG8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A2K6CN04_A0A2K6CN04_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0G3_F7F0G3_MACMU_9544 and tr_A0A2K5YFB3_A0A2K5YFB3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HIP5_F7HIP5_MACMU_9544 and tr_A0A096NR53_A0A096NR53_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HIP5_F7HIP5_MACMU_9544 and tr_A0A2K5LLN7_A0A2K5LLN7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HIP5_F7HIP5_MACMU_9544 and tr_A0A2K6C757_A0A2K6C757_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZTF3_H0ZTF3_TAEGU_59729 and tr_A0A218V3F4_A0A218V3F4_9PASE_299123 are exactly identical! WARNING: Sequences tr_F6YWW2_F6YWW2_XENTR_8364 and tr_F7CQ34_F7CQ34_XENTR_8364 are exactly identical! WARNING: Sequences tr_F6YYK8_F6YYK8_XENTR_8364 and tr_F6ZUB2_F6ZUB2_XENTR_8364 are exactly identical! WARNING: Sequences tr_F7C6P1_F7C6P1_XENTR_8364 and tr_L7N360_L7N360_XENTR_8364 are exactly identical! WARNING: Sequences tr_G1L423_G1L423_AILME_9646 and tr_A0A384D8H6_A0A384D8H6_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3W1B7_M3W1B7_FELCA_9685 and tr_M3X7P2_M3X7P2_FELCA_9685 are exactly identical! WARNING: Sequences tr_U3K1U9_U3K1U9_FICAL_59894 and tr_A0A091UN01_A0A091UN01_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3K1U9_U3K1U9_FICAL_59894 and tr_A0A087R8T9_A0A087R8T9_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3K1U9_U3K1U9_FICAL_59894 and tr_A0A091G093_A0A091G093_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A087YK63_A0A087YK63_POEFO_48698 and tr_A0A096MA92_A0A096MA92_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096MBX7_A0A096MBX7_POEFO_48698 and tr_A0A096MF25_A0A096MF25_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096NRG7_A0A096NRG7_PAPAN_9555 and tr_A0A2K5P4D4_A0A2K5P4D4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NRG7_A0A096NRG7_PAPAN_9555 and tr_A0A2K6A832_A0A2K6A832_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MUJ3_A0A151MUJ3_ALLMI_8496 and tr_A0A1U8CYG7_A0A1U8CYG7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NSD4_A0A151NSD4_ALLMI_8496 and tr_A0A1U7RC16_A0A1U7RC16_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091V027_A0A091V027_NIPNI_128390 and tr_A0A0A0B2A2_A0A0A0B2A2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LUR9_A0A2I0LUR9_COLLI_8932 and tr_A0A1V4KQU2_A0A1V4KQU2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M8Q6_A0A2I0M8Q6_COLLI_8932 and tr_A0A1V4JRS7_A0A1V4JRS7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3PHS3_A0A1S3PHS3_SALSA_8030 and tr_A0A060WLY4_A0A060WLY4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PN29_A0A1S3PN29_SALSA_8030 and tr_A0A060WPA1_A0A060WPA1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PN73_A0A1S3PN73_SALSA_8030 and tr_A0A060Z9D7_A0A060Z9D7_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1L8HNK9_A0A1L8HNK9_XENLA_8355 and tr_A0A1L8HNL8_A0A1L8HNL8_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HNK9_A0A1L8HNK9_XENLA_8355 and tr_A0A1L8HNN1_A0A1L8HNN1_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HWV6_A0A1L8HWV6_XENLA_8355 and tr_A0A1L8HX05_A0A1L8HX05_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HWY4_A0A1L8HWY4_XENLA_8355 and tr_A0A1L8HWZ7_A0A1L8HWZ7_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HWY4_A0A1L8HWY4_XENLA_8355 and tr_A0A1L8HX21_A0A1L8HX21_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HX01_A0A1L8HX01_XENLA_8355 and tr_A0A1L8HXP5_A0A1L8HXP5_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1L8HX30_A0A1L8HX30_XENLA_8355 and tr_A0A1L8HXB8_A0A1L8HXB8_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A226MUZ3_A0A226MUZ3_CALSU_9009 and tr_A0A226PY14_A0A226PY14_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NCJ9_A0A226NCJ9_CALSU_9009 and tr_A0A226PTQ1_A0A226PTQ1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NJV4_A0A226NJV4_CALSU_9009 and tr_A0A226PUM7_A0A226PUM7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5N1A1_A0A2K5N1A1_CERAT_9531 and tr_A0A2K5XZP1_A0A2K5XZP1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4CKT0_A0A2U4CKT0_TURTR_9739 and tr_A0A384A1F2_A0A384A1F2_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9LAE6_A0A2Y9LAE6_DELLE_9749 and tr_A0A2Y9F7F6_A0A2Y9F7F6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9LAE6_A0A2Y9LAE6_DELLE_9749 and tr_A0A384A0Y1_A0A384A0Y1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9P854_A0A2Y9P854_DELLE_9749 and tr_A0A383YMS0_A0A383YMS0_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 150 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/Q8N1P7/3_mltree/Q8N1P7.raxml.reduced.phy Alignment comprises 1 partitions and 121 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 121 / 121 Gaps: 1.85 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.rba Parallelization scheme autoconfig: 2 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 999 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -208103.304378] Initial branch length optimization [00:00:03 -169938.362498] Model parameter optimization (eps = 10.000000) [00:00:37 -169696.221568] AUTODETECT spr round 1 (radius: 5) [00:02:41 -111440.689406] AUTODETECT spr round 2 (radius: 10) [00:04:47 -75821.457878] AUTODETECT spr round 3 (radius: 15) [00:07:06 -57361.501371] AUTODETECT spr round 4 (radius: 20) [00:09:34 -50557.534467] AUTODETECT spr round 5 (radius: 25) [00:12:28 -49071.375647] SPR radius for FAST iterations: 25 (autodetect) [00:12:28 -49071.375647] Model parameter optimization (eps = 3.000000) [00:12:45 -48961.318898] FAST spr round 1 (radius: 25) [00:14:49 -38149.517786] FAST spr round 2 (radius: 25) [00:16:32 -36521.228792] FAST spr round 3 (radius: 25) [00:18:09 -35962.695535] FAST spr round 4 (radius: 25) [00:19:49 -35821.083444] FAST spr round 5 (radius: 25) [00:21:16 -35798.757361] FAST spr round 6 (radius: 25) [00:22:41 -35798.757233] Model parameter optimization (eps = 1.000000) [00:22:55 -35793.368279] SLOW spr round 1 (radius: 5) [00:24:45 -35774.046504] SLOW spr round 2 (radius: 5) [00:26:33 -35773.253949] SLOW spr round 3 (radius: 5) [00:28:21 -35773.253612] SLOW spr round 4 (radius: 10) [00:30:05 -35773.253551] SLOW spr round 5 (radius: 15) [00:32:31 -35773.253508] SLOW spr round 6 (radius: 20) [00:35:43 -35773.253469] SLOW spr round 7 (radius: 25) [00:39:45 -35773.253434] Model parameter optimization (eps = 0.100000) [00:39:58] [worker #0] ML tree search #1, logLikelihood: -35772.957838 [00:39:58 -208253.510451] Initial branch length optimization [00:40:01 -170209.546517] Model parameter optimization (eps = 10.000000) [00:40:30 -170038.733400] AUTODETECT spr round 1 (radius: 5) [00:42:35 -107172.855571] AUTODETECT spr round 2 (radius: 10) [00:44:44 -76232.922906] AUTODETECT spr round 3 (radius: 15) [00:46:55 -62889.041235] AUTODETECT spr round 4 (radius: 20) [00:49:32 -51387.798197] AUTODETECT spr round 5 (radius: 25) [00:50:52] [worker #1] ML tree search #2, logLikelihood: -35783.489038 [00:52:33 -45023.084889] SPR radius for FAST iterations: 25 (autodetect) [00:52:33 -45023.084889] Model parameter optimization (eps = 3.000000) [00:52:51 -44897.525798] FAST spr round 1 (radius: 25) [00:54:52 -36492.209519] FAST spr round 2 (radius: 25) [00:56:34 -35847.649297] FAST spr round 3 (radius: 25) [00:58:11 -35796.322542] FAST spr round 4 (radius: 25) [00:59:41 -35792.242366] FAST spr round 5 (radius: 25) [01:01:05 -35790.833053] FAST spr round 6 (radius: 25) [01:02:32 -35787.513339] FAST spr round 7 (radius: 25) [01:03:56 -35787.015641] FAST spr round 8 (radius: 25) [01:05:19 -35787.015571] Model parameter optimization (eps = 1.000000) [01:05:28 -35785.860225] SLOW spr round 1 (radius: 5) [01:07:17 -35776.265488] SLOW spr round 2 (radius: 5) [01:09:03 -35775.844043] SLOW spr round 3 (radius: 5) [01:10:45 -35775.842360] SLOW spr round 4 (radius: 10) [01:12:29 -35775.113513] SLOW spr round 5 (radius: 5) [01:14:37 -35775.113242] SLOW spr round 6 (radius: 10) [01:16:30 -35775.113040] SLOW spr round 7 (radius: 15) [01:18:52 -35775.112869] SLOW spr round 8 (radius: 20) [01:22:22 -35775.112723] SLOW spr round 9 (radius: 25) [01:26:31 -35775.112598] Model parameter optimization (eps = 0.100000) [01:26:35] [worker #0] ML tree search #3, logLikelihood: -35775.101912 [01:26:35 -209504.412131] Initial branch length optimization [01:26:38 -171266.907955] Model parameter optimization (eps = 10.000000) [01:27:18 -171043.900357] AUTODETECT spr round 1 (radius: 5) [01:29:24 -109860.372330] AUTODETECT spr round 2 (radius: 10) [01:29:38] [worker #1] ML tree search #4, logLikelihood: -35778.266655 [01:31:32 -74558.158895] AUTODETECT spr round 3 (radius: 15) [01:33:46 -57220.832235] AUTODETECT spr round 4 (radius: 20) [01:36:16 -49654.353320] AUTODETECT spr round 5 (radius: 25) [01:38:47 -42889.337408] SPR radius for FAST iterations: 25 (autodetect) [01:38:47 -42889.337408] Model parameter optimization (eps = 3.000000) [01:39:13 -42776.429648] FAST spr round 1 (radius: 25) [01:41:14 -36236.048814] FAST spr round 2 (radius: 25) [01:42:56 -35862.845646] FAST spr round 3 (radius: 25) [01:44:32 -35818.540929] FAST spr round 4 (radius: 25) [01:46:03 -35807.113097] FAST spr round 5 (radius: 25) [01:47:31 -35807.112868] Model parameter optimization (eps = 1.000000) [01:47:43 -35805.636811] SLOW spr round 1 (radius: 5) [01:49:34 -35796.988145] SLOW spr round 2 (radius: 5) [01:51:24 -35795.147496] SLOW spr round 3 (radius: 5) [01:53:12 -35795.147331] SLOW spr round 4 (radius: 10) [01:54:59 -35795.147226] SLOW spr round 5 (radius: 15) [01:57:25 -35795.028695] SLOW spr round 6 (radius: 5) [01:59:43 -35795.028628] SLOW spr round 7 (radius: 10) [02:01:44 -35794.482037] SLOW spr round 8 (radius: 5) [02:03:51 -35793.782792] SLOW spr round 9 (radius: 5) [02:05:45 -35793.782752] SLOW spr round 10 (radius: 10) [02:07:29 -35793.782725] SLOW spr round 11 (radius: 15) [02:09:51 -35793.782700] SLOW spr round 12 (radius: 20) [02:13:09 -35793.782678] SLOW spr round 13 (radius: 25) [02:17:22 -35793.782657] Model parameter optimization (eps = 0.100000) [02:17:29] [worker #0] ML tree search #5, logLikelihood: -35793.490912 [02:17:29 -207504.943980] Initial branch length optimization [02:17:32 -169617.538007] Model parameter optimization (eps = 10.000000) [02:17:57 -169401.327761] AUTODETECT spr round 1 (radius: 5) [02:20:00 -110238.456420] AUTODETECT spr round 2 (radius: 10) [02:22:06 -74917.297860] AUTODETECT spr round 3 (radius: 15) [02:23:20] [worker #1] ML tree search #6, logLikelihood: -35764.488208 [02:24:24 -58978.002781] AUTODETECT spr round 4 (radius: 20) [02:26:58 -48836.652320] AUTODETECT spr round 5 (radius: 25) [02:29:26 -46574.732465] SPR radius for FAST iterations: 25 (autodetect) [02:29:26 -46574.732465] Model parameter optimization (eps = 3.000000) [02:29:45 -46453.383295] FAST spr round 1 (radius: 25) [02:31:46 -36824.872771] FAST spr round 2 (radius: 25) [02:33:30 -35898.696761] FAST spr round 3 (radius: 25) [02:35:06 -35810.295820] FAST spr round 4 (radius: 25) [02:36:37 -35804.507780] FAST spr round 5 (radius: 25) [02:38:05 -35802.058820] FAST spr round 6 (radius: 25) [02:39:30 -35802.058640] Model parameter optimization (eps = 1.000000) [02:39:43 -35790.157131] SLOW spr round 1 (radius: 5) [02:41:34 -35771.053347] SLOW spr round 2 (radius: 5) [02:43:22 -35767.887931] SLOW spr round 3 (radius: 5) [02:45:07 -35767.887619] SLOW spr round 4 (radius: 10) [02:46:51 -35767.887519] SLOW spr round 5 (radius: 15) [02:49:21 -35767.887518] SLOW spr round 6 (radius: 20) [02:52:34 -35767.887517] SLOW spr round 7 (radius: 25) [02:56:22 -35767.887517] Model parameter optimization (eps = 0.100000) [02:56:34] [worker #0] ML tree search #7, logLikelihood: -35766.444255 [02:56:34 -208086.971140] Initial branch length optimization [02:56:37 -170115.760092] Model parameter optimization (eps = 10.000000) [02:57:03 -169895.866529] AUTODETECT spr round 1 (radius: 5) [02:59:07 -109132.900296] AUTODETECT spr round 2 (radius: 10) [03:01:13 -75384.044041] AUTODETECT spr round 3 (radius: 15) [03:03:28 -59265.864801] AUTODETECT spr round 4 (radius: 20) [03:06:00 -49008.544606] AUTODETECT spr round 5 (radius: 25) [03:09:23] [worker #1] ML tree search #8, logLikelihood: -35767.925103 [03:09:29 -44613.175538] SPR radius for FAST iterations: 25 (autodetect) [03:09:29 -44613.175538] Model parameter optimization (eps = 3.000000) [03:09:46 -44497.026400] FAST spr round 1 (radius: 25) [03:11:43 -36340.221749] FAST spr round 2 (radius: 25) [03:13:21 -35821.565658] FAST spr round 3 (radius: 25) [03:14:52 -35800.970964] FAST spr round 4 (radius: 25) [03:16:22 -35797.678043] FAST spr round 5 (radius: 25) [03:17:49 -35795.078307] FAST spr round 6 (radius: 25) [03:19:12 -35794.136367] FAST spr round 7 (radius: 25) [03:20:37 -35794.135778] Model parameter optimization (eps = 1.000000) [03:20:48 -35792.686179] SLOW spr round 1 (radius: 5) [03:22:37 -35778.469480] SLOW spr round 2 (radius: 5) [03:24:23 -35772.220658] SLOW spr round 3 (radius: 5) [03:26:10 -35768.404775] SLOW spr round 4 (radius: 5) [03:27:57 -35768.404733] SLOW spr round 5 (radius: 10) [03:29:42 -35768.404717] SLOW spr round 6 (radius: 15) [03:32:11 -35768.117113] SLOW spr round 7 (radius: 5) [03:34:27 -35767.078561] SLOW spr round 8 (radius: 5) [03:36:27 -35767.078550] SLOW spr round 9 (radius: 10) [03:38:14 -35766.743461] SLOW spr round 10 (radius: 5) [03:40:22 -35764.942078] SLOW spr round 11 (radius: 5) [03:42:17 -35764.942045] SLOW spr round 12 (radius: 10) [03:44:02 -35764.942045] SLOW spr round 13 (radius: 15) [03:46:28 -35763.501483] SLOW spr round 14 (radius: 5) [03:48:42 -35763.501480] SLOW spr round 15 (radius: 10) [03:50:40 -35763.501480] SLOW spr round 16 (radius: 15) [03:53:00 -35763.501480] SLOW spr round 17 (radius: 20) [03:56:17 -35763.501479] SLOW spr round 18 (radius: 25) [04:00:11 -35763.501479] Model parameter optimization (eps = 0.100000) [04:00:15] [worker #1] ML tree search #10, logLikelihood: -35739.746218 [04:00:22] [worker #0] ML tree search #9, logLikelihood: -35762.736202 [04:00:22 -210415.808970] Initial branch length optimization [04:00:25 -170922.722254] Model parameter optimization (eps = 10.000000) [04:00:52 -170755.672646] AUTODETECT spr round 1 (radius: 5) [04:02:58 -108448.462127] AUTODETECT spr round 2 (radius: 10) [04:05:06 -75618.160204] AUTODETECT spr round 3 (radius: 15) [04:07:28 -58877.955871] AUTODETECT spr round 4 (radius: 20) [04:10:10 -47826.631005] AUTODETECT spr round 5 (radius: 25) [04:12:39 -44881.097120] SPR radius for FAST iterations: 25 (autodetect) [04:12:39 -44881.097120] Model parameter optimization (eps = 3.000000) [04:13:04 -44733.901461] FAST spr round 1 (radius: 25) [04:15:05 -36574.020042] FAST spr round 2 (radius: 25) [04:16:45 -35851.790801] FAST spr round 3 (radius: 25) [04:18:17 -35790.442662] FAST spr round 4 (radius: 25) [04:19:45 -35785.935480] FAST spr round 5 (radius: 25) [04:21:10 -35785.934908] Model parameter optimization (eps = 1.000000) [04:21:22 -35776.330975] SLOW spr round 1 (radius: 5) [04:23:09 -35757.567905] SLOW spr round 2 (radius: 5) [04:24:57 -35755.106045] SLOW spr round 3 (radius: 5) [04:26:43 -35754.405925] SLOW spr round 4 (radius: 5) [04:28:27 -35754.212818] SLOW spr round 5 (radius: 5) [04:30:11 -35754.211805] SLOW spr round 6 (radius: 10) [04:31:54 -35754.211687] SLOW spr round 7 (radius: 15) [04:34:20 -35754.211656] SLOW spr round 8 (radius: 20) [04:37:41 -35751.565982] SLOW spr round 9 (radius: 5) [04:39:44 -35751.526225] SLOW spr round 10 (radius: 10) [04:41:18 -35751.526185] SLOW spr round 11 (radius: 15) [04:43:05 -35751.526114] SLOW spr round 12 (radius: 20) [04:45:44 -35751.526105] SLOW spr round 13 (radius: 25) [04:48:56 -35751.526097] Model parameter optimization (eps = 0.100000) [04:49:02] [worker #0] ML tree search #11, logLikelihood: -35749.962038 [04:49:02 -208224.127269] Initial branch length optimization [04:49:04 -169604.765744] Model parameter optimization (eps = 10.000000) [04:49:28 -169400.138207] AUTODETECT spr round 1 (radius: 5) [04:51:08 -109824.323915] AUTODETECT spr round 2 (radius: 10) [04:52:52 -73187.610395] AUTODETECT spr round 3 (radius: 15) [04:54:48 -55164.667095] AUTODETECT spr round 4 (radius: 20) [04:55:54] [worker #1] ML tree search #12, logLikelihood: -35765.256933 [04:56:55 -46331.805191] AUTODETECT spr round 5 (radius: 25) [04:59:21 -42692.555483] SPR radius for FAST iterations: 25 (autodetect) [04:59:21 -42692.555483] Model parameter optimization (eps = 3.000000) [04:59:36 -42569.836018] FAST spr round 1 (radius: 25) [05:01:12 -36381.316154] FAST spr round 2 (radius: 25) [05:02:35 -35841.926582] FAST spr round 3 (radius: 25) [05:03:56 -35815.683839] FAST spr round 4 (radius: 25) [05:05:11 -35815.134941] FAST spr round 5 (radius: 25) [05:06:25 -35815.134837] Model parameter optimization (eps = 1.000000) [05:06:34 -35805.532738] SLOW spr round 1 (radius: 5) [05:08:08 -35797.655060] SLOW spr round 2 (radius: 5) [05:09:42 -35795.570281] SLOW spr round 3 (radius: 5) [05:11:16 -35795.569960] SLOW spr round 4 (radius: 10) [05:12:45 -35795.569881] SLOW spr round 5 (radius: 15) [05:14:47 -35793.658217] SLOW spr round 6 (radius: 5) [05:16:44 -35793.658112] SLOW spr round 7 (radius: 10) [05:18:26 -35786.857399] SLOW spr round 8 (radius: 5) [05:20:14 -35786.857364] SLOW spr round 9 (radius: 10) [05:21:48 -35786.857356] SLOW spr round 10 (radius: 15) [05:23:44 -35786.857324] SLOW spr round 11 (radius: 20) [05:26:27 -35785.241056] SLOW spr round 12 (radius: 5) [05:28:25 -35782.838110] SLOW spr round 13 (radius: 5) [05:30:08 -35782.838072] SLOW spr round 14 (radius: 10) [05:31:40 -35779.707710] SLOW spr round 15 (radius: 5) [05:33:27 -35779.707629] SLOW spr round 16 (radius: 10) [05:35:02 -35779.707624] SLOW spr round 17 (radius: 15) [05:36:57 -35779.707622] SLOW spr round 18 (radius: 20) [05:38:31] [worker #1] ML tree search #14, logLikelihood: -35793.368842 [05:39:40 -35779.589685] SLOW spr round 19 (radius: 5) [05:41:36 -35778.346402] SLOW spr round 20 (radius: 5) [05:43:19 -35777.590809] SLOW spr round 21 (radius: 5) [05:44:54 -35777.590775] SLOW spr round 22 (radius: 10) [05:46:23 -35777.590773] SLOW spr round 23 (radius: 15) [05:48:23 -35777.590772] SLOW spr round 24 (radius: 20) [05:51:03 -35777.590770] SLOW spr round 25 (radius: 25) [05:54:20 -35777.590769] Model parameter optimization (eps = 0.100000) [05:54:32] [worker #0] ML tree search #13, logLikelihood: -35776.857227 [05:54:32 -207816.179199] Initial branch length optimization [05:54:34 -170020.415162] Model parameter optimization (eps = 10.000000) [05:55:00 -169740.945959] AUTODETECT spr round 1 (radius: 5) [05:56:47 -110504.896185] AUTODETECT spr round 2 (radius: 10) [05:58:38 -72048.069604] AUTODETECT spr round 3 (radius: 15) [06:00:33 -54194.696671] AUTODETECT spr round 4 (radius: 20) [06:02:43 -48796.819128] AUTODETECT spr round 5 (radius: 25) [06:05:04 -44327.863481] SPR radius for FAST iterations: 25 (autodetect) [06:05:04 -44327.863481] Model parameter optimization (eps = 3.000000) [06:05:28 -44206.143494] FAST spr round 1 (radius: 25) [06:07:08 -36996.922261] FAST spr round 2 (radius: 25) [06:08:34 -35960.698606] FAST spr round 3 (radius: 25) [06:09:55 -35808.026323] FAST spr round 4 (radius: 25) [06:11:14 -35774.523066] FAST spr round 5 (radius: 25) [06:12:28 -35772.344465] FAST spr round 6 (radius: 25) [06:13:40 -35772.343776] Model parameter optimization (eps = 1.000000) [06:13:49 -35769.051962] SLOW spr round 1 (radius: 5) [06:15:22 -35762.703260] SLOW spr round 2 (radius: 5) [06:16:55 -35758.910235] SLOW spr round 3 (radius: 5) [06:18:27 -35757.596489] SLOW spr round 4 (radius: 5) [06:19:56 -35757.274662] SLOW spr round 5 (radius: 5) [06:21:24 -35756.518611] SLOW spr round 6 (radius: 5) [06:22:52 -35756.517485] SLOW spr round 7 (radius: 10) [06:24:22 -35754.891385] SLOW spr round 8 (radius: 5) [06:26:10 -35754.890267] SLOW spr round 9 (radius: 10) [06:27:47 -35754.795485] SLOW spr round 10 (radius: 15) [06:29:50 -35754.794861] SLOW spr round 11 (radius: 20) [06:32:55 -35754.794339] SLOW spr round 12 (radius: 25) [06:36:35 -35754.793896] Model parameter optimization (eps = 0.100000) [06:36:40] [worker #1] ML tree search #16, logLikelihood: -35768.274647 [06:36:42] [worker #0] ML tree search #15, logLikelihood: -35754.668139 [06:36:42 -206522.538628] Initial branch length optimization [06:36:44 -168875.465094] Model parameter optimization (eps = 10.000000) [06:37:09 -168718.451627] AUTODETECT spr round 1 (radius: 5) [06:38:56 -108420.997279] AUTODETECT spr round 2 (radius: 10) [06:40:47 -72506.670240] AUTODETECT spr round 3 (radius: 15) [06:42:42 -56597.979085] AUTODETECT spr round 4 (radius: 20) [06:44:44 -49987.444525] AUTODETECT spr round 5 (radius: 25) [06:47:21 -46568.956516] SPR radius for FAST iterations: 25 (autodetect) [06:47:21 -46568.956516] Model parameter optimization (eps = 3.000000) [06:47:36 -46419.338295] FAST spr round 1 (radius: 25) [06:49:19 -38366.160825] FAST spr round 2 (radius: 25) [06:50:50 -36860.243500] FAST spr round 3 (radius: 25) [06:52:14 -36101.857419] FAST spr round 4 (radius: 25) [06:53:34 -35818.571665] FAST spr round 5 (radius: 25) [06:54:51 -35811.930229] FAST spr round 6 (radius: 25) [06:56:05 -35810.893978] FAST spr round 7 (radius: 25) [06:57:18 -35810.893970] Model parameter optimization (eps = 1.000000) [06:57:28 -35803.245651] SLOW spr round 1 (radius: 5) [06:59:00 -35791.843948] SLOW spr round 2 (radius: 5) [07:00:32 -35791.842367] SLOW spr round 3 (radius: 10) [07:02:02 -35790.159127] SLOW spr round 4 (radius: 5) [07:03:55 -35787.893110] SLOW spr round 5 (radius: 5) [07:05:36 -35785.845111] SLOW spr round 6 (radius: 5) [07:07:08 -35785.845034] SLOW spr round 7 (radius: 10) [07:08:37 -35785.599631] SLOW spr round 8 (radius: 5) [07:10:26 -35785.599552] SLOW spr round 9 (radius: 10) [07:12:02 -35785.458717] SLOW spr round 10 (radius: 5) [07:13:49 -35784.795873] SLOW spr round 11 (radius: 5) [07:15:26 -35784.795867] SLOW spr round 12 (radius: 10) [07:15:55] [worker #1] ML tree search #18, logLikelihood: -35768.588663 [07:16:55 -35784.795867] SLOW spr round 13 (radius: 15) [07:18:59 -35784.699920] SLOW spr round 14 (radius: 20) [07:21:47 -35784.699917] SLOW spr round 15 (radius: 25) [07:25:11 -35784.699917] Model parameter optimization (eps = 0.100000) [07:25:14] [worker #0] ML tree search #17, logLikelihood: -35784.687730 [07:25:14 -209145.791799] Initial branch length optimization [07:25:17 -171137.231732] Model parameter optimization (eps = 10.000000) [07:25:43 -170939.948074] AUTODETECT spr round 1 (radius: 5) [07:27:33 -107676.616932] AUTODETECT spr round 2 (radius: 10) [07:29:24 -75372.992012] AUTODETECT spr round 3 (radius: 15) [07:31:19 -57555.772785] AUTODETECT spr round 4 (radius: 20) [07:33:30 -50244.147699] AUTODETECT spr round 5 (radius: 25) [07:35:41 -50063.316947] SPR radius for FAST iterations: 25 (autodetect) [07:35:41 -50063.316947] Model parameter optimization (eps = 3.000000) [07:36:02 -49940.101361] FAST spr round 1 (radius: 25) [07:37:42 -40748.052734] FAST spr round 2 (radius: 25) [07:39:07 -37983.622752] FAST spr round 3 (radius: 25) [07:40:29 -36707.232082] FAST spr round 4 (radius: 25) [07:41:48 -35949.453561] FAST spr round 5 (radius: 25) [07:43:05 -35791.050657] FAST spr round 6 (radius: 25) [07:44:19 -35784.729620] FAST spr round 7 (radius: 25) [07:45:29 -35784.729543] Model parameter optimization (eps = 1.000000) [07:45:40 -35775.893502] SLOW spr round 1 (radius: 5) [07:47:11 -35761.991571] SLOW spr round 2 (radius: 5) [07:48:43 -35761.096167] SLOW spr round 3 (radius: 5) [07:50:13 -35761.095007] SLOW spr round 4 (radius: 10) [07:51:42 -35759.866748] SLOW spr round 5 (radius: 5) [07:53:34 -35756.488711] SLOW spr round 6 (radius: 5) [07:55:14 -35756.488690] SLOW spr round 7 (radius: 10) [07:56:45 -35756.396578] SLOW spr round 8 (radius: 15) [07:58:49 -35756.396570] SLOW spr round 9 (radius: 20) [08:01:45 -35756.396562] SLOW spr round 10 (radius: 25) [08:05:00 -35756.396555] Model parameter optimization (eps = 0.100000) [08:05:07] [worker #0] ML tree search #19, logLikelihood: -35756.030257 [08:11:03] [worker #1] ML tree search #20, logLikelihood: -35758.549678 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.177661,0.369386) (0.295613,0.741757) (0.311578,1.123385) (0.215148,1.696876) 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: -35739.746218 AIC score: 75481.492436 / AICc score: 8087485.492436 / BIC score: 81075.869318 Free parameters (model + branch lengths): 2001 WARNING: Number of free parameters (K=2001) is larger than alignment size (n=121). 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/Q8N1P7/3_mltree/Q8N1P7.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N1P7/3_mltree/Q8N1P7.raxml.log Analysis started: 03-Jul-2021 18:46:17 / finished: 04-Jul-2021 02:57:21 Elapsed time: 29464.127 seconds Consumed energy: 2287.710 Wh (= 11 km in an electric car, or 57 km with an e-scooter!)