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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 16-Jul-2021 08:17:05 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/2_msa/A6NIR3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/2_msa/A6NIR3_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 325 sites WARNING: Sequences tr_B4Q581_B4Q581_DROSI_7240 and sp_Q9NGC3_CEG1A_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R1D5_B4R1D5_DROSI_7240 and tr_Q9VCQ6_Q9VCQ6_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5NW09_A0A1D5NW09_CHICK_9031 and tr_A0A226N9G5_A0A226N9G5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PI31_A0A1D5PI31_CHICK_9031 and tr_A0A226MW26_A0A226MW26_CALSU_9009 are exactly identical! WARNING: Sequences tr_D3YUJ3_D3YUJ3_MOUSE_10090 and tr_F1M4U0_F1M4U0_RAT_10116 are exactly identical! WARNING: Sequences tr_D3YUJ3_D3YUJ3_MOUSE_10090 and tr_M3WU07_M3WU07_FELCA_9685 are exactly identical! WARNING: Sequences tr_D3YUJ3_D3YUJ3_MOUSE_10090 and tr_A0A1U7RG82_A0A1U7RG82_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q3UHD9_AGAP2_MOUSE_10090 and sp_Q8CGU4_AGAP2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q6ZQK5_ACAP2_MOUSE_10090 and sp_Q5FVC7_ACAP2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XN33_M3XN33_MUSPF_9669 and tr_G1M9J5_G1M9J5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XN33_M3XN33_MUSPF_9669 and tr_A0A2U3WAQ4_A0A2U3WAQ4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XN33_M3XN33_MUSPF_9669 and tr_A0A2U3XPM5_A0A2U3XPM5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XN33_M3XN33_MUSPF_9669 and tr_A0A2Y9JDN5_A0A2Y9JDN5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XQM3_M3XQM3_MUSPF_9669 and tr_A0A2U3WLQ0_A0A2U3WLQ0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XQM3_M3XQM3_MUSPF_9669 and tr_A0A2Y9JB63_A0A2Y9JB63_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XXB2_M3XXB2_MUSPF_9669 and tr_G1LS46_G1LS46_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXB2_M3XXB2_MUSPF_9669 and tr_A0A2Y9KBY1_A0A2Y9KBY1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YBK3_M3YBK3_MUSPF_9669 and tr_G1M4Z7_G1M4Z7_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_H2PCF0_H2PCF0_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_H2QP05_H2QP05_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_F7C4E1_F7C4E1_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and sp_Q15057_ACAP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_A0A0D9R8T7_A0A0D9R8T7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_A0A2R9BJT9_A0A2R9BJT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_A0A2Y9SVZ3_A0A2Y9SVZ3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3HAK8_A0A2I3HAK8_NOMLE_61853 and tr_A0A2I3SFN4_A0A2I3SFN4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HAK8_A0A2I3HAK8_NOMLE_61853 and tr_A0A2R8ZI72_A0A2R8ZI72_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_H2PP27_H2PP27_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_H2QVM6_H2QVM6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and sp_Q96P47_AGAP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_A0A1D5QZQ4_A0A1D5QZQ4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_G7P219_G7P219_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_A0A2K5MPF4_A0A2K5MPF4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_A0A2K6CGD5_A0A2K6CGD5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QW60_G1QW60_NOMLE_61853 and tr_A0A2R9A9E7_A0A2R9A9E7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1P606_G1P606_MYOLU_59463 and tr_F1PD13_F1PD13_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1P606_G1P606_MYOLU_59463 and tr_F6UJP0_F6UJP0_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1P606_G1P606_MYOLU_59463 and tr_A0A287AC08_A0A287AC08_PIG_9823 are exactly identical! WARNING: Sequences tr_G1P606_G1P606_MYOLU_59463 and tr_L5K1F3_L5K1F3_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1P606_G1P606_MYOLU_59463 and tr_A0A2Y9NPI9_A0A2Y9NPI9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_K7CJ94_K7CJ94_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and sp_Q8N7R7_CCYL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A2R9B0L8_A0A2R9B0L8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Z8K9_A0A2I2Z8K9_GORGO_9595 and tr_K7ASV6_K7ASV6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z8K9_A0A2I2Z8K9_GORGO_9595 and sp_Q96P50_ACAP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A1D5R919_A0A1D5R919_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_G7NYR9_G7NYR9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A2I3NCN3_A0A2I3NCN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A2K5MSE0_A0A2K5MSE0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A2K6DUQ0_A0A2K6DUQ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A2K5Y267_A0A2K5Y267_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1SG54_G1SG54_RABIT_9986 and tr_A0A2U3VBN3_A0A2U3VBN3_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A0R3NEV5_A0A0R3NEV5_DROPS_46245 and tr_B4GP69_B4GP69_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2RD06_H2RD06_PANTR_9598 and tr_A0A2R9BF19_A0A2R9BF19_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DTP8_F7DTP8_HORSE_9796 and tr_A0A337S596_A0A337S596_FELCA_9685 are exactly identical! WARNING: Sequences tr_F7DTP8_F7DTP8_HORSE_9796 and tr_A0A2Y9KLD6_A0A2Y9KLD6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_W5PXZ1_W5PXZ1_SHEEP_9940 and tr_E1BI41_E1BI41_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4AC91_M4AC91_XIPMA_8083 and tr_A0A096M8N7_A0A096M8N7_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NDC8_A0A158NDC8_ATTCE_12957 and tr_A0A151I1C4_A0A151I1C4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NGM0_A0A158NGM0_ATTCE_12957 and tr_A0A195B7V5_A0A195B7V5_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5QP64_A0A1D5QP64_MACMU_9544 and tr_A0A096NQI1_A0A096NQI1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QP64_A0A1D5QP64_MACMU_9544 and tr_A0A2K5M907_A0A2K5M907_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QP64_A0A1D5QP64_MACMU_9544 and tr_A0A2K6CHJ1_A0A2K6CHJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_F7HYI9_F7HYI9_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_A0A096MLE9_A0A096MLE9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_A0A0D9RCH8_A0A0D9RCH8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_A0A2K5MQH6_A0A2K5MQH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_A0A2K6CK18_A0A2K6CK18_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AUG1_F7AUG1_MACMU_9544 and tr_A0A2K6A287_A0A2K6A287_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A096NYF0_A0A096NYF0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A0D9QX81_A0A0D9QX81_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A2K5KRJ1_A0A2K5KRJ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A2K6E4Y1_A0A2K6E4Y1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A096N8D9_A0A096N8D9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A0D9R1N9_A0A0D9R1N9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A2K5LEQ3_A0A2K5LEQ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A2K6BBK1_A0A2K6BBK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A2K5Z1S6_A0A2K5Z1S6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HLN4_F7HLN4_MACMU_9544 and tr_G7PTG4_G7PTG4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HLN4_F7HLN4_MACMU_9544 and tr_A0A2K6BQW9_A0A2K6BQW9_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_E5SZN3_E5SZN3_TRISP_6334 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V0RWT6_A0A0V0RWT6_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V1CQC3_A0A0V1CQC3_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V0WCH1_A0A0V0WCH1_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V0VAY5_A0A0V0VAY5_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V1A319_A0A0V1A319_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V1NTD5_A0A0V1NTD5_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V0UD97_A0A0V0UD97_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0YZJ0_H0YZJ0_TAEGU_59729 and tr_A0A093PU69_A0A093PU69_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZAT0_H0ZAT0_TAEGU_59729 and tr_U3K220_U3K220_FICAL_59894 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUW0_A0A2D0SUW0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUW8_A0A2D0SUW8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUX1_A0A2D0SUX1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A0A1MZM2_A0A0A1MZM2_9FUNG_58291 and tr_A0A367JWG0_A0A367JWG0_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091FDD2_A0A091FDD2_CORBR_85066 and tr_A0A091I371_A0A091I371_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A087RDD6_A0A087RDD6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A091VXV9_A0A091VXV9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A0A0AMY3_A0A0A0AMY3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VCX5_A0A091VCX5_NIPNI_128390 and tr_A0A087R7X0_A0A087R7X0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1S3SYR6_A0A1S3SYR6_SALSA_8030 and tr_A0A060W0V4_A0A060W0V4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D1UMV8_A0A1D1UMV8_RAMVA_947166 and tr_A0A1D1URJ9_A0A1D1URJ9_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226N2B4_A0A226N2B4_CALSU_9009 and tr_A0A226N842_A0A226N842_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N8P5_A0A226N8P5_CALSU_9009 and tr_A0A226PSY0_A0A226PSY0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PHC7_A0A2D0PHC7_ICTPU_7998 and tr_A0A2D0PIN5_A0A2D0PIN5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QQT0_A0A2D0QQT0_ICTPU_7998 and tr_A0A2D0QR01_A0A2D0QR01_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QQT0_A0A2D0QQT0_ICTPU_7998 and tr_A0A2D0QRA4_A0A2D0QRA4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBA0_A0A2D0RBA0_ICTPU_7998 and tr_W5UG84_W5UG84_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUF0_A0A2D0RUF0_ICTPU_7998 and tr_A0A2D0RVC0_A0A2D0RVC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUF0_A0A2D0RUF0_ICTPU_7998 and tr_A0A2D0RVY9_A0A2D0RVY9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3B5_A0A2D0S3B5_ICTPU_7998 and tr_A0A2D0S3B7_A0A2D0S3B7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3B5_A0A2D0S3B5_ICTPU_7998 and tr_A0A2D0S3D4_A0A2D0S3D4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3B5_A0A2D0S3B5_ICTPU_7998 and tr_A0A2D0S4V5_A0A2D0S4V5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SI70_A0A2D0SI70_ICTPU_7998 and tr_W5UCZ6_W5UCZ6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SLM4_A0A2D0SLM4_ICTPU_7998 and tr_A0A2D0SM82_A0A2D0SM82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SLM4_A0A2D0SLM4_ICTPU_7998 and tr_A0A2D0SMV3_A0A2D0SMV3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SR08_A0A2D0SR08_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SR14_A0A2D0SR14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SR19_A0A2D0SR19_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SS55_A0A2D0SS55_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CKI3_A0A2U4CKI3_TURTR_9739 and tr_A0A2Y9LAK1_A0A2Y9LAK1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CKI3_A0A2U4CKI3_TURTR_9739 and tr_A0A2Y9SIW5_A0A2Y9SIW5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CKI3_A0A2U4CKI3_TURTR_9739 and tr_A0A383ZYH5_A0A383ZYH5_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3W1L5_A0A2U3W1L5_ODORO_9708 and tr_A0A2U3Y924_A0A2U3Y924_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9MW19_A0A2Y9MW19_DELLE_9749 and tr_A0A2Y9EX31_A0A2Y9EX31_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9NDS3_A0A2Y9NDS3_DELLE_9749 and tr_A0A383ZY70_A0A383ZY70_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 125 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.reduced.phy Alignment comprises 1 partitions and 325 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 325 / 325 Gaps: 11.40 % Invariant sites: 0.31 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 325 / 26000 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -508916.370992] Initial branch length optimization [00:00:10 -417482.611178] Model parameter optimization (eps = 10.000000) [00:01:17 -416568.584025] AUTODETECT spr round 1 (radius: 5) [00:05:46 -266370.139704] AUTODETECT spr round 2 (radius: 10) [00:10:17 -186905.991473] AUTODETECT spr round 3 (radius: 15) [00:15:03 -156007.709154] AUTODETECT spr round 4 (radius: 20) [00:20:16 -145766.983988] AUTODETECT spr round 5 (radius: 25) [00:26:41 -133376.426823] SPR radius for FAST iterations: 25 (autodetect) [00:26:41 -133376.426823] Model parameter optimization (eps = 3.000000) [00:27:24 -133261.393497] FAST spr round 1 (radius: 25) [00:32:08 -101588.292347] FAST spr round 2 (radius: 25) [00:35:53 -99360.526767] FAST spr round 3 (radius: 25) [00:38:58 -98910.229655] FAST spr round 4 (radius: 25) [00:41:55 -98892.676719] FAST spr round 5 (radius: 25) [00:44:34 -98889.286132] FAST spr round 6 (radius: 25) [00:47:09 -98889.285655] Model parameter optimization (eps = 1.000000) [00:47:31 -98881.591673] SLOW spr round 1 (radius: 5) [00:51:13 -98858.641896] SLOW spr round 2 (radius: 5) [00:54:51 -98853.163156] SLOW spr round 3 (radius: 5) [00:58:29 -98845.966257] SLOW spr round 4 (radius: 5) [01:01:57 -98845.960621] SLOW spr round 5 (radius: 10) [01:05:32 -98842.745077] SLOW spr round 6 (radius: 5) [01:09:53 -98841.681117] SLOW spr round 7 (radius: 5) [01:13:42 -98841.680729] SLOW spr round 8 (radius: 10) [01:17:24 -98841.680656] SLOW spr round 9 (radius: 15) [01:22:47 -98841.053340] SLOW spr round 10 (radius: 5) [01:27:17 -98841.052698] SLOW spr round 11 (radius: 10) [01:31:30 -98841.052587] SLOW spr round 12 (radius: 15) [01:32:24] [worker #4] ML tree search #5, logLikelihood: -98843.856402 [01:36:41 -98841.052549] SLOW spr round 13 (radius: 20) [01:42:21] [worker #3] ML tree search #4, logLikelihood: -98844.875246 [01:44:36 -98841.052525] SLOW spr round 14 (radius: 25) [01:44:51] [worker #1] ML tree search #2, logLikelihood: -98856.889612 [01:54:29 -98841.052503] Model parameter optimization (eps = 0.100000) [01:54:42] [worker #0] ML tree search #1, logLikelihood: -98840.781665 [01:54:42 -508587.176965] Initial branch length optimization [01:54:50 -413478.529405] Model parameter optimization (eps = 10.000000) [01:56:04 -412692.038223] AUTODETECT spr round 1 (radius: 5) [02:00:36 -265298.509984] AUTODETECT spr round 2 (radius: 10) [02:01:08] [worker #2] ML tree search #3, logLikelihood: -98868.590821 [02:05:02 -189734.179955] AUTODETECT spr round 3 (radius: 15) [02:09:55 -151224.910899] AUTODETECT spr round 4 (radius: 20) [02:15:26 -138024.336998] AUTODETECT spr round 5 (radius: 25) [02:21:56 -134167.361318] SPR radius for FAST iterations: 25 (autodetect) [02:21:56 -134167.361318] Model parameter optimization (eps = 3.000000) [02:22:30 -134062.243284] FAST spr round 1 (radius: 25) [02:27:34 -103187.751081] FAST spr round 2 (radius: 25) [02:31:02 -99172.221126] FAST spr round 3 (radius: 25) [02:34:11 -98935.725573] FAST spr round 4 (radius: 25) [02:37:06 -98913.882666] FAST spr round 5 (radius: 25) [02:39:45 -98913.199795] FAST spr round 6 (radius: 25) [02:42:21 -98913.199161] Model parameter optimization (eps = 1.000000) [02:42:40 -98899.637248] SLOW spr round 1 (radius: 5) [02:46:18 -98868.535669] SLOW spr round 2 (radius: 5) [02:49:50 -98864.954970] SLOW spr round 3 (radius: 5) [02:53:20 -98864.222024] SLOW spr round 4 (radius: 5) [02:56:45 -98864.222002] SLOW spr round 5 (radius: 10) [03:00:19 -98861.920265] SLOW spr round 6 (radius: 5) [03:04:36 -98861.873748] SLOW spr round 7 (radius: 10) [03:08:38 -98861.873705] SLOW spr round 8 (radius: 15) [03:13:56 -98861.873682] SLOW spr round 9 (radius: 20) [03:21:57 -98861.873661] SLOW spr round 10 (radius: 25) [03:32:02 -98861.873639] Model parameter optimization (eps = 0.100000) [03:32:10] [worker #0] ML tree search #6, logLikelihood: -98861.820975 [03:32:10 -507656.775667] Initial branch length optimization [03:32:20 -415312.578737] Model parameter optimization (eps = 10.000000) [03:33:42 -414532.991692] AUTODETECT spr round 1 (radius: 5) [03:38:13 -261618.585856] AUTODETECT spr round 2 (radius: 10) [03:42:51 -184994.693855] AUTODETECT spr round 3 (radius: 15) [03:47:51 -146618.171867] AUTODETECT spr round 4 (radius: 20) [03:51:24] [worker #4] ML tree search #10, logLikelihood: -98852.814213 [03:53:41 -128721.259188] AUTODETECT spr round 5 (radius: 25) [04:00:06 -121019.463543] SPR radius for FAST iterations: 25 (autodetect) [04:00:06 -121019.463543] Model parameter optimization (eps = 3.000000) [04:00:50 -120893.806640] FAST spr round 1 (radius: 25) [04:05:34 -100321.974298] FAST spr round 2 (radius: 25) [04:08:55 -99034.898732] FAST spr round 3 (radius: 25) [04:11:40] [worker #3] ML tree search #9, logLikelihood: -98921.651219 [04:12:01 -98886.058433] FAST spr round 4 (radius: 25) [04:13:16] [worker #2] ML tree search #8, logLikelihood: -98850.176027 [04:14:54 -98880.794595] FAST spr round 5 (radius: 25) [04:17:32 -98879.810429] FAST spr round 6 (radius: 25) [04:20:06 -98879.810086] Model parameter optimization (eps = 1.000000) [04:20:29 -98873.750601] SLOW spr round 1 (radius: 5) [04:24:17 -98853.336845] SLOW spr round 2 (radius: 5) [04:24:40] [worker #1] ML tree search #7, logLikelihood: -98846.496886 [04:27:51 -98852.440454] SLOW spr round 3 (radius: 5) [04:31:17 -98852.439929] SLOW spr round 4 (radius: 10) [04:34:57 -98847.257557] SLOW spr round 5 (radius: 5) [04:39:15 -98847.252817] SLOW spr round 6 (radius: 10) [04:43:19 -98847.252397] SLOW spr round 7 (radius: 15) [04:48:43 -98846.620220] SLOW spr round 8 (radius: 5) [04:53:17 -98846.619366] SLOW spr round 9 (radius: 10) [04:57:34 -98846.619181] SLOW spr round 10 (radius: 15) [05:02:56 -98846.619086] SLOW spr round 11 (radius: 20) [05:11:13 -98846.619005] SLOW spr round 12 (radius: 25) [05:21:40 -98846.618927] Model parameter optimization (eps = 0.100000) [05:21:54] [worker #0] ML tree search #11, logLikelihood: -98846.457287 [05:21:55 -511887.899896] Initial branch length optimization [05:22:02 -419691.643096] Model parameter optimization (eps = 10.000000) [05:24:03 -418911.172212] AUTODETECT spr round 1 (radius: 5) [05:28:32 -262748.586208] AUTODETECT spr round 2 (radius: 10) [05:33:04 -190912.577124] AUTODETECT spr round 3 (radius: 15) [05:37:54 -155781.917959] AUTODETECT spr round 4 (radius: 20) [05:43:31 -144428.085129] AUTODETECT spr round 5 (radius: 25) [05:49:53 -130418.301580] SPR radius for FAST iterations: 25 (autodetect) [05:49:53 -130418.301580] Model parameter optimization (eps = 3.000000) [05:50:33 -130287.340371] FAST spr round 1 (radius: 25) [05:55:37 -101852.245426] FAST spr round 2 (radius: 25) [05:58:48] [worker #3] ML tree search #14, logLikelihood: -98844.088599 [05:59:26 -99097.620353] FAST spr round 3 (radius: 25) [06:01:32] [worker #4] ML tree search #15, logLikelihood: -98858.165602 [06:02:55 -98935.314851] FAST spr round 4 (radius: 25) [06:05:57 -98908.766074] FAST spr round 5 (radius: 25) [06:08:45 -98893.553755] FAST spr round 6 (radius: 25) [06:11:22 -98893.552708] Model parameter optimization (eps = 1.000000) [06:11:45 -98884.010418] SLOW spr round 1 (radius: 5) [06:15:21 -98868.852272] SLOW spr round 2 (radius: 5) [06:18:15] [worker #2] ML tree search #13, logLikelihood: -98924.850644 [06:18:55 -98868.284914] SLOW spr round 3 (radius: 5) [06:22:21 -98868.284650] SLOW spr round 4 (radius: 10) [06:23:17] [worker #1] ML tree search #12, logLikelihood: -98843.605128 [06:25:57 -98866.476801] SLOW spr round 5 (radius: 5) [06:30:16 -98866.475266] SLOW spr round 6 (radius: 10) [06:34:21 -98866.474996] SLOW spr round 7 (radius: 15) [06:39:52 -98864.739331] SLOW spr round 8 (radius: 5) [06:44:33 -98863.422686] SLOW spr round 9 (radius: 5) [06:48:34 -98863.422432] SLOW spr round 10 (radius: 10) [06:52:23 -98863.422368] SLOW spr round 11 (radius: 15) [06:58:03 -98860.273019] SLOW spr round 12 (radius: 5) [07:02:37 -98860.225267] SLOW spr round 13 (radius: 10) [07:06:58 -98858.502536] SLOW spr round 14 (radius: 5) [07:11:09 -98858.502471] SLOW spr round 15 (radius: 10) [07:15:09 -98858.502406] SLOW spr round 16 (radius: 15) [07:20:38 -98858.502340] SLOW spr round 17 (radius: 20) [07:29:02 -98858.502274] SLOW spr round 18 (radius: 25) [07:39:58 -98858.502208] Model parameter optimization (eps = 0.100000) [07:40:06] [worker #0] ML tree search #16, logLikelihood: -98858.440516 [07:50:43] [worker #2] ML tree search #18, logLikelihood: -98856.282485 [08:01:18] [worker #4] ML tree search #20, logLikelihood: -99658.482722 [08:26:24] [worker #3] ML tree search #19, logLikelihood: -98849.962702 [08:42:04] [worker #1] ML tree search #17, logLikelihood: -98933.714016 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.193503,0.348986) (0.176972,0.497946) (0.431392,0.968075) (0.198133,2.153742) 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: -98840.781665 AIC score: 201691.563330 / AICc score: 8245751.563330 / BIC score: 209278.132821 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=325). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 251 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NIR3/3_mltree/A6NIR3.raxml.log Analysis started: 16-Jul-2021 08:17:05 / finished: 16-Jul-2021 16:59:10 Elapsed time: 31324.762 seconds