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 12-Jul-2021 15:45:46 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/2_msa/Q9UBH6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/2_msa/Q9UBH6_trimmed_msa.fasta [00:00:00] Loaded alignment with 987 taxa and 165 sites WARNING: Sequences tr_B4QIU5_B4QIU5_DROSI_7240 and tr_B4HUL2_B4HUL2_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QIU5_B4QIU5_DROSI_7240 and tr_B3MB29_B3MB29_DROAN_7217 are exactly identical! WARNING: Sequences tr_B4QIU5_B4QIU5_DROSI_7240 and tr_A0A1W4UXC1_A0A1W4UXC1_DROFC_30025 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_G1MVZ7_G1MVZ7_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_U3J8F1_U3J8F1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A0Q3X8A6_A0A0Q3X8A6_AMAAE_12930 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A091JNH0_A0A091JNH0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A091UY74_A0A091UY74_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A087QVJ3_A0A087QVJ3_APTFO_9233 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A091VGC4_A0A091VGC4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A091GM79_A0A091GM79_9AVES_55661 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A0A0B0A3_A0A0A0B0A3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A2I0MC77_A0A2I0MC77_COLLI_8932 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A091IAA7_A0A091IAA7_CALAN_9244 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A226N0U0_A0A226N0U0_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C6K2_E1C6K2_CHICK_9031 and tr_A0A226PVY1_A0A226PVY1_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3YJ66_M3YJ66_MUSPF_9669 and tr_A0A2Y9JTQ5_A0A2Y9JTQ5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B6HMN0_B6HMN0_PENRW_500485 and tr_A0A1V6Z437_A0A1V6Z437_PENNA_60175 are exactly identical! WARNING: Sequences tr_Q9VRR2_Q9VRR2_DROME_7227 and tr_B4MMK2_B4MMK2_DROWI_7260 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_G3S7A2_G3S7A2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_H2N4H5_H2N4H5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_H2Q0Q1_H2Q0Q1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and sp_Q9UBH6_XPR1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_G7MF56_G7MF56_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_G7NXI5_G7NXI5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A096MQA0_A0A096MQA0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A3Q0EF36_A0A3Q0EF36_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A2K5N6D4_A0A2K5N6D4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A2K6C4X2_A0A2K6C4X2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A2K5ZXB9_A0A2K5ZXB9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S1L8_G1S1L8_NOMLE_61853 and tr_A0A2R8ZLI4_A0A2R8ZLI4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1SDK2_G1SDK2_RABIT_9986 and tr_F6PMF3_F6PMF3_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1SDK2_G1SDK2_RABIT_9986 and tr_M3WFX0_M3WFX0_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1SDK2_G1SDK2_RABIT_9986 and tr_A0A2Y9DE21_A0A2Y9DE21_TRIMA_127582 are exactly identical! WARNING: Sequences tr_Q29E65_Q29E65_DROPS_46245 and tr_B4HAV0_B4HAV0_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29H73_Q29H73_DROPS_46245 and tr_B4H074_B4H074_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A179UX88_A0A179UX88_BLAGS_559298 and tr_C5GR03_C5GR03_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FC72_F9FC72_FUSOF_660025 and tr_A0A0D2XV44_A0A0D2XV44_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FC72_F9FC72_FUSOF_660025 and tr_N4UIF6_N4UIF6_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FC72_F9FC72_FUSOF_660025 and tr_X0D0Z8_X0D0Z8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FC72_F9FC72_FUSOF_660025 and tr_A0A2H3T8Y3_A0A2H3T8Y3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A087ZYJ9_A0A087ZYJ9_APIME_7460 and tr_A0A2A3E3H5_A0A2A3E3H5_APICC_94128 are exactly identical! WARNING: Sequences tr_J3LI80_J3LI80_ORYBR_4533 and tr_B8AEH8_B8AEH8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_J3LI80_J3LI80_ORYBR_4533 and tr_I1P5E0_I1P5E0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_J3LI80_J3LI80_ORYBR_4533 and sp_Q6K991_PHO12_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0K0JN72_A0A0K0JN72_BRUMA_6279 and tr_A0A0R3QSF8_A0A0R3QSF8_9BILA_42155 are exactly identical! WARNING: Sequences tr_G7XGZ3_G7XGZ3_ASPKW_1033177 and tr_A0A146F1A4_A0A146F1A4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_B8BMT3_B8BMT3_ORYSI_39946 and tr_Q2QMQ9_Q2QMQ9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_W4YTG9_W4YTG9_STRPU_7668 and tr_W4Z750_W4Z750_STRPU_7668 are exactly identical! WARNING: Sequences tr_H1A430_H1A430_TAEGU_59729 and tr_A0A091EXF8_A0A091EXF8_CORBR_85066 are exactly identical! WARNING: Sequences tr_H1A430_H1A430_TAEGU_59729 and tr_A0A218V5K6_A0A218V5K6_9PASE_299123 are exactly identical! WARNING: Sequences tr_G0MKY4_G0MKY4_CAEBE_135651 and tr_E3LZG4_E3LZG4_CAERE_31234 are exactly identical! WARNING: Sequences tr_G0MKY4_G0MKY4_CAEBE_135651 and tr_A8XSF9_A8XSF9_CAEBR_6238 are exactly identical! WARNING: Sequences tr_G0MKY4_G0MKY4_CAEBE_135651 and tr_A0A261BV41_A0A261BV41_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G0MKY4_G0MKY4_CAEBE_135651 and tr_A0A2G5USW1_A0A2G5USW1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_M4DLL4_M4DLL4_BRARP_51351 and tr_A0A078J482_A0A078J482_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DLL4_M4DLL4_BRARP_51351 and tr_A0A0D3E7N7_A0A0D3E7N7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M4DT43_M4DT43_BRARP_51351 and tr_A0A078IZG5_A0A078IZG5_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4E7M7_M4E7M7_BRARP_51351 and tr_A0A078I6Y4_A0A078I6Y4_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4EDK4_M4EDK4_BRARP_51351 and tr_A0A078JYI6_A0A078JYI6_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F566_M4F566_BRARP_51351 and tr_A0A078G3L2_A0A078G3L2_BRANA_3708 are exactly identical! WARNING: Sequences tr_S0E0H8_S0E0H8_GIBF5_1279085 and tr_A0A365MJJ2_A0A365MJJ2_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A0A3B6NUQ4_A0A3B6NUQ4_WHEAT_4565 and tr_A0A3B6QNP3_A0A3B6QNP3_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015JCH2_A0A015JCH2_9GLOM_1432141 and tr_A0A2H5SD87_A0A2H5SD87_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067EEZ7_A0A067EEZ7_CITSI_2711 and tr_V4UVN6_V4UVN6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067EEZ7_A0A067EEZ7_CITSI_2711 and tr_A0A2H5NV30_A0A2H5NV30_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067F8N9_A0A067F8N9_CITSI_2711 and tr_V4W423_V4W423_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067F8N9_A0A067F8N9_CITSI_2711 and tr_A0A2H5QHI9_A0A2H5QHI9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067FS23_A0A067FS23_CITSI_2711 and tr_V4ST36_V4ST36_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A094GG97_A0A094GG97_9PEZI_1420912 and tr_A0A1B8GLD4_A0A1B8GLD4_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A2VDM7_A0A0A2VDM7_BEABA_1245745 and tr_A0A2N6NNJ7_A0A2N6NNJ7_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0D2PMX6_A0A0D2PMX6_GOSRA_29730 and tr_A0A1U8MFU8_A0A1U8MFU8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RNZ0_A0A0D2RNZ0_GOSRA_29730 and tr_A0A1U8HWN1_A0A1U8HWN1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RP15_A0A0D2RP15_GOSRA_29730 and tr_A0A1U8KAF1_A0A1U8KAF1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2T8J6_A0A0D2T8J6_GOSRA_29730 and tr_A0A1U8NB93_A0A1U8NB93_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0L1JFB0_A0A0L1JFB0_ASPNO_1509407 and tr_A0A1F7ZST4_A0A1F7ZST4_9EURO_109264 are exactly identical! WARNING: Sequences tr_A0A0A1NE92_A0A0A1NE92_9FUNG_58291 and tr_A0A367JF66_A0A367JF66_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0L9TLZ8_A0A0L9TLZ8_PHAAN_3914 and tr_A0A1S3ULK0_A0A1S3ULK0_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A093HBU2_A0A093HBU2_STRCA_441894 and tr_A0A099Z1A5_A0A099Z1A5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0XC63_A0A0V0XC63_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0VN33_A0A0V0VN33_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V1LQI8_A0A0V1LQI8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V1A4G7_A0A0V1A4G7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V1P9E4_A0A0V1P9E4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DGY5_A0A0V1DGY5_TRIBR_45882 and tr_A0A0V0UC85_A0A0V0UC85_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1NAH5_A0A0V1NAH5_9BILA_268474 and tr_A0A0V1I9Q3_A0A0V1I9Q3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A117DYJ9_A0A117DYJ9_ASPNG_5061 and tr_A0A1L9MXY2_A0A1L9MXY2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A117DYJ9_A0A117DYJ9_ASPNG_5061 and tr_A0A317UQE1_A0A317UQE1_9EURO_1448314 are exactly identical! WARNING: Sequences tr_I1RQ06_I1RQ06_GIBZE_229533 and tr_A0A2T4GP44_A0A2T4GP44_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1S4B309_A0A1S4B309_TOBAC_4097 and tr_A0A314KJF6_A0A314KJF6_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4B309_A0A1S4B309_TOBAC_4097 and tr_A0A1U7X944_A0A1U7X944_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CGC2_A0A1S4CGC2_TOBAC_4097 and tr_A0A1U7WQ83_A0A1U7WQ83_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CMJ5_A0A1S4CMJ5_TOBAC_4097 and tr_A0A1U7XTI2_A0A1U7XTI2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CTV1_A0A1S4CTV1_TOBAC_4097 and tr_A0A1U7WMG1_A0A1U7WMG1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CUJ1_A0A1S4CUJ1_TOBAC_4097 and tr_A0A1U7WB30_A0A1U7WB30_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3LWA1_A0A1S3LWA1_SALSA_8030 and tr_A0A060VPT0_A0A060VPT0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A3Q0EZY5_A0A3Q0EZY5_VIGRR_3916 and tr_A0A3Q0F4H2_A0A3Q0F4H2_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1B8ANM1_A0A1B8ANM1_FUSPO_36050 and tr_A0A2L2THU5_A0A2L2THU5_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A1D1UI70_A0A1D1UI70_RAMVA_947166 and tr_A0A1D1UND4_A0A1D1UND4_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1U8J675_A0A1U8J675_GOSHI_3635 and tr_A0A1U8PB50_A0A1U8PB50_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A060WLS9_A0A060WLS9_ONCMY_8022 and tr_A0A060YGL8_A0A060YGL8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1U8GD54_A0A1U8GD54_CAPAN_4072 and tr_A0A2G3CSA7_A0A2G3CSA7_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G2YCM2_A0A2G2YCM2_CAPAN_4072 and tr_A0A2G3B6L2_A0A2G3B6L2_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G3ACD4_A0A2G3ACD4_CAPAN_4072 and tr_A0A2G3D9K4_A0A2G3D9K4_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G3ACI7_A0A2G3ACI7_CAPAN_4072 and tr_A0A2G3D9P2_A0A2G3D9P2_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2P5EQW8_A0A2P5EQW8_TREOI_63057 and tr_A0A2P5E1M3_A0A2P5E1M3_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2P5F662_A0A2P5F662_TREOI_63057 and tr_A0A2P5D646_A0A2P5D646_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2P5G0C3_A0A2P5G0C3_TREOI_63057 and tr_A0A2P5BZC5_A0A2P5BZC5_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2U1QG66_A0A2U1QG66_ARTAN_35608 and tr_A0A2U1QNQ7_A0A2U1QNQ7_ARTAN_35608 are exactly identical! WARNING: Sequences tr_A0A2U3VP67_A0A2U3VP67_ODORO_9708 and tr_A0A2U3XZQ7_A0A2U3XZQ7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2V5IAU5_A0A2V5IAU5_9EURO_1450541 and tr_A0A2V5I377_A0A2V5I377_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 111 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/Q9UBH6/3_mltree/Q9UBH6.raxml.reduced.phy Alignment comprises 1 partitions and 165 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 165 / 165 Gaps: 6.16 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.rba Parallelization scheme autoconfig: 3 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 987 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 165 / 13200 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -284602.312448] Initial branch length optimization [00:00:04 -235888.026018] Model parameter optimization (eps = 10.000000) [00:01:11 -234293.805856] AUTODETECT spr round 1 (radius: 5) [00:04:01 -164478.404947] AUTODETECT spr round 2 (radius: 10) [00:07:02 -126604.036177] AUTODETECT spr round 3 (radius: 15) [00:10:15 -104121.556948] AUTODETECT spr round 4 (radius: 20) [00:13:37 -90909.244109] AUTODETECT spr round 5 (radius: 25) [00:17:41 -87394.302093] SPR radius for FAST iterations: 25 (autodetect) [00:17:41 -87394.302093] Model parameter optimization (eps = 3.000000) [00:18:08 -87260.299833] FAST spr round 1 (radius: 25) [00:21:28 -74095.919049] FAST spr round 2 (radius: 25) [00:23:59 -73457.141268] FAST spr round 3 (radius: 25) [00:26:14 -73311.006594] FAST spr round 4 (radius: 25) [00:28:21 -73281.105112] FAST spr round 5 (radius: 25) [00:30:21 -73277.038301] FAST spr round 6 (radius: 25) [00:32:17 -73275.454086] FAST spr round 7 (radius: 25) [00:34:13 -73275.453942] Model parameter optimization (eps = 1.000000) [00:34:34 -73268.166708] SLOW spr round 1 (radius: 5) [00:37:07 -73241.561291] SLOW spr round 2 (radius: 5) [00:39:37 -73234.314063] SLOW spr round 3 (radius: 5) [00:42:04 -73231.709235] SLOW spr round 4 (radius: 5) [00:44:26 -73231.709121] SLOW spr round 5 (radius: 10) [00:46:51 -73230.482346] SLOW spr round 6 (radius: 5) [00:49:47 -73230.481233] SLOW spr round 7 (radius: 10) [00:52:22 -73230.481148] SLOW spr round 8 (radius: 15) [00:55:33 -73230.481117] SLOW spr round 9 (radius: 20) [00:59:34 -73230.419245] SLOW spr round 10 (radius: 25) [01:04:18 -73230.418876] Model parameter optimization (eps = 0.100000) [01:04:27] [worker #0] ML tree search #1, logLikelihood: -73230.372251 [01:04:27 -286253.263701] Initial branch length optimization [01:04:33 -235828.985806] Model parameter optimization (eps = 10.000000) [01:05:18 -234253.309797] AUTODETECT spr round 1 (radius: 5) [01:08:10 -164692.179917] AUTODETECT spr round 2 (radius: 10) [01:11:11 -124215.770682] AUTODETECT spr round 3 (radius: 15) [01:14:23 -102089.135762] AUTODETECT spr round 4 (radius: 20) [01:17:50 -94167.689765] AUTODETECT spr round 5 (radius: 25) [01:21:30 -89232.692114] SPR radius for FAST iterations: 25 (autodetect) [01:21:30 -89232.692114] Model parameter optimization (eps = 3.000000) [01:22:03 -89123.831526] FAST spr round 1 (radius: 25) [01:25:19 -74561.403734] FAST spr round 2 (radius: 25) [01:27:49 -73644.295791] FAST spr round 3 (radius: 25) [01:30:01 -73382.000417] FAST spr round 4 (radius: 25) [01:32:07 -73348.879517] FAST spr round 5 (radius: 25) [01:34:06 -73342.099832] FAST spr round 6 (radius: 25) [01:36:01 -73341.174187] FAST spr round 7 (radius: 25) [01:37:54 -73341.174128] Model parameter optimization (eps = 1.000000) [01:38:08 -73335.483665] SLOW spr round 1 (radius: 5) 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 14-Jul-2021 01:47:49 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/2_msa/Q9UBH6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.rba [00:00:00] Alignment comprises 987 taxa, 1 partitions and 165 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 165 / 165 Gaps: 6.16 % Invariant sites: 0.00 % Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -73335.48, ML trees: 1, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 165 / 13200 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -73335.483665] SPR radius for FAST iterations: 25 (autodetect) [00:00:00 -73335.483665] SLOW spr round 1 (radius: 5) [00:02:19 -73310.346559] SLOW spr round 2 (radius: 5) [00:04:41 -73299.762313] SLOW spr round 3 (radius: 5) [00:07:05 -73288.601880] SLOW spr round 4 (radius: 5) [00:09:23 -73288.595522] SLOW spr round 5 (radius: 10) [00:11:44 -73288.501030] SLOW spr round 6 (radius: 15) [00:15:10 -73285.459616] SLOW spr round 7 (radius: 5) [00:18:13 -73284.741094] SLOW spr round 8 (radius: 5) [00:18:48] [worker #2] ML tree search #3, logLikelihood: -73223.766600 [00:20:52 -73284.740337] SLOW spr round 9 (radius: 10) [00:23:19 -73284.736588] SLOW spr round 10 (radius: 15) [00:26:39 -73284.736397] SLOW spr round 11 (radius: 20) [00:28:45] [worker #1] ML tree search #2, logLikelihood: -73241.818561 [00:31:03 -73284.736257] SLOW spr round 12 (radius: 25) [00:36:26 -73284.736151] Model parameter optimization (eps = 0.100000) [00:36:37] [worker #0] ML tree search #4, logLikelihood: -73284.146613 [00:36:37 -286739.230529] Initial branch length optimization [00:36:41 -235974.265983] Model parameter optimization (eps = 10.000000) [00:37:33 -234439.893119] AUTODETECT spr round 1 (radius: 5) [00:40:23 -163414.427722] AUTODETECT spr round 2 (radius: 10) [00:43:20 -124595.990215] AUTODETECT spr round 3 (radius: 15) [00:46:27 -106632.379878] AUTODETECT spr round 4 (radius: 20) [00:49:44 -97103.396630] AUTODETECT spr round 5 (radius: 25) [00:53:17 -94341.133725] SPR radius for FAST iterations: 25 (autodetect) [00:53:17 -94341.133725] Model parameter optimization (eps = 3.000000) [00:53:52 -94131.307564] FAST spr round 1 (radius: 25) [00:57:00 -80521.835355] FAST spr round 2 (radius: 25) [00:59:25 -76378.824259] FAST spr round 3 (radius: 25) [01:01:35 -73778.361734] FAST spr round 4 (radius: 25) [01:03:38 -73273.669943] FAST spr round 5 (radius: 25) [01:05:37 -73241.832213] FAST spr round 6 (radius: 25) [01:07:27 -73238.261885] FAST spr round 7 (radius: 25) [01:09:15 -73237.160497] FAST spr round 8 (radius: 25) [01:11:03 -73237.160385] Model parameter optimization (eps = 1.000000) [01:11:18 -73233.045211] SLOW spr round 1 (radius: 5) [01:13:39 -73212.267662] SLOW spr round 2 (radius: 5) [01:16:02 -73208.457974] SLOW spr round 3 (radius: 5) [01:18:20 -73208.457743] SLOW spr round 4 (radius: 10) [01:20:42 -73207.336864] SLOW spr round 5 (radius: 5) [01:23:35 -73207.336144] SLOW spr round 6 (radius: 10) [01:26:11 -73207.336070] SLOW spr round 7 (radius: 15) [01:29:31 -73207.336023] SLOW spr round 8 (radius: 20) [01:34:07 -73207.088169] SLOW spr round 9 (radius: 5) [01:37:11 -73207.088124] SLOW spr round 10 (radius: 10) [01:38:47] [worker #1] ML tree search #6, logLikelihood: -73362.639263 [01:39:57 -73207.088081] SLOW spr round 11 (radius: 15) [01:43:14 -73207.088039] SLOW spr round 12 (radius: 20) [01:47:49 -73207.087997] SLOW spr round 13 (radius: 25) [01:53:30 -73207.087956] Model parameter optimization (eps = 0.100000) [01:53:37] [worker #0] ML tree search #5, logLikelihood: -73207.074346 [01:53:37 -285580.817871] Initial branch length optimization [01:53:42 -237329.481898] Model parameter optimization (eps = 10.000000) [01:54:27 -235889.622800] AUTODETECT spr round 1 (radius: 5) [01:57:16 -165302.935206] AUTODETECT spr round 2 (radius: 10) [02:00:17 -126722.204436] AUTODETECT spr round 3 (radius: 15) [02:02:59] [worker #2] ML tree search #7, logLikelihood: -73205.669114 [02:03:24 -106652.674579] AUTODETECT spr round 4 (radius: 20) [02:06:50 -96308.592630] AUTODETECT spr round 5 (radius: 25) [02:10:56 -92114.702593] SPR radius for FAST iterations: 25 (autodetect) [02:10:56 -92114.702593] Model parameter optimization (eps = 3.000000) [02:11:22 -92001.243895] FAST spr round 1 (radius: 25) [02:14:42 -77254.167590] FAST spr round 2 (radius: 25) [02:17:15 -76406.212547] FAST spr round 3 (radius: 25) [02:19:35 -74941.044858] FAST spr round 4 (radius: 25) [02:21:45 -74124.183724] FAST spr round 5 (radius: 25) [02:23:47 -73624.976747] FAST spr round 6 (radius: 25) [02:25:49 -73278.002846] FAST spr round 7 (radius: 25) [02:27:43 -73266.328249] FAST spr round 8 (radius: 25) [02:29:31 -73266.327180] Model parameter optimization (eps = 1.000000) [02:29:51 -73244.821544] SLOW spr round 1 (radius: 5) [02:32:14 -73210.633746] SLOW spr round 2 (radius: 5) [02:34:37 -73194.135420] SLOW spr round 3 (radius: 5) [02:36:59 -73193.626945] SLOW spr round 4 (radius: 5) [02:39:18 -73193.626368] SLOW spr round 5 (radius: 10) [02:41:40 -73192.569285] SLOW spr round 6 (radius: 5) [02:44:34 -73192.569189] SLOW spr round 7 (radius: 10) [02:47:08 -73192.569129] SLOW spr round 8 (radius: 15) [02:50:26 -73192.500830] SLOW spr round 9 (radius: 20) [02:51:02] [worker #1] ML tree search #9, logLikelihood: -73224.349109 [02:54:54 -73192.500779] SLOW spr round 10 (radius: 25) [03:00:11 -73192.222797] SLOW spr round 11 (radius: 5) [03:03:18 -73192.222749] SLOW spr round 12 (radius: 10) [03:06:06 -73192.222712] SLOW spr round 13 (radius: 15) [03:09:21 -73192.222685] SLOW spr round 14 (radius: 20) [03:13:48 -73192.222658] SLOW spr round 15 (radius: 25) [03:19:02 -73192.222632] Model parameter optimization (eps = 0.100000) [03:19:12] [worker #0] ML tree search #8, logLikelihood: -73191.680965 [03:19:12 -285983.018543] Initial branch length optimization [03:19:17 -236118.780129] Model parameter optimization (eps = 10.000000) [03:20:07 -234478.620853] AUTODETECT spr round 1 (radius: 5) [03:22:54 -165037.744485] AUTODETECT spr round 2 (radius: 10) [03:25:53 -124679.462183] AUTODETECT spr round 3 (radius: 15) [03:29:06 -104297.154144] AUTODETECT spr round 4 (radius: 20) [03:32:33 -89494.616718] AUTODETECT spr round 5 (radius: 25) [03:36:35 -86174.821514] SPR radius for FAST iterations: 25 (autodetect) [03:36:35 -86174.821514] Model parameter optimization (eps = 3.000000) [03:37:03 -86027.646209] FAST spr round 1 (radius: 25) [03:40:10 -73983.575162] FAST spr round 2 (radius: 25) [03:42:34 -73528.442888] FAST spr round 3 (radius: 25) [03:43:32] [worker #2] ML tree search #10, logLikelihood: -73227.751699 [03:44:43 -73282.746495] FAST spr round 4 (radius: 25) [03:46:44 -73263.941176] FAST spr round 5 (radius: 25) [03:48:39 -73260.009662] FAST spr round 6 (radius: 25) [03:50:30 -73257.430018] FAST spr round 7 (radius: 25) [03:52:19 -73257.429884] Model parameter optimization (eps = 1.000000) [03:52:39 -73252.809806] SLOW spr round 1 (radius: 5) [03:55:05 -73230.163638] SLOW spr round 2 (radius: 5) [03:57:30 -73228.953178] SLOW spr round 3 (radius: 5) [03:59:54 -73228.952868] SLOW spr round 4 (radius: 10) [04:02:21 -73227.175910] SLOW spr round 5 (radius: 5) [04:05:19 -73226.258797] SLOW spr round 6 (radius: 5) [04:07:55 -73226.246383] SLOW spr round 7 (radius: 10) [04:10:23 -73226.243656] SLOW spr round 8 (radius: 15) [04:13:48 -73222.968823] SLOW spr round 9 (radius: 5) [04:16:52 -73222.313459] SLOW spr round 10 (radius: 5) [04:19:32 -73222.313367] SLOW spr round 11 (radius: 10) [04:22:01 -73222.313348] SLOW spr round 12 (radius: 15) [04:25:23 -73222.313342] SLOW spr round 13 (radius: 20) [04:29:52 -73220.646165] SLOW spr round 14 (radius: 5) [04:32:58 -73220.645357] SLOW spr round 15 (radius: 10) [04:35:44 -73220.645324] SLOW spr round 16 (radius: 15) [04:39:01 -73220.645322] SLOW spr round 17 (radius: 20) [04:43:32 -73220.645320] SLOW spr round 18 (radius: 25) [04:48:54 -73220.645318] Model parameter optimization (eps = 0.100000) [04:48:59] [worker #0] ML tree search #11, logLikelihood: -73220.634219 [04:49:00 -287573.100663] Initial branch length optimization [04:49:04 -237295.922029] Model parameter optimization (eps = 10.000000) [04:50:04 -235721.003276] AUTODETECT spr round 1 (radius: 5) [04:52:52 -164725.508703] AUTODETECT spr round 2 (radius: 10) [04:55:50 -122936.974443] AUTODETECT spr round 3 (radius: 15) [04:59:03 -105254.595788] AUTODETECT spr round 4 (radius: 20) [05:02:53 -90201.440123] AUTODETECT spr round 5 (radius: 25) [05:06:20] [worker #2] ML tree search #13, logLikelihood: -73204.535878 [05:07:18 -86841.782553] SPR radius for FAST iterations: 25 (autodetect) [05:07:18 -86841.782553] Model parameter optimization (eps = 3.000000) [05:07:58 -86690.891737] FAST spr round 1 (radius: 25) [05:10:27] [worker #1] ML tree search #12, logLikelihood: -73290.648701 [05:11:05 -73829.309835] FAST spr round 2 (radius: 25) [05:13:24 -73327.053990] FAST spr round 3 (radius: 25) [05:15:30 -73273.526127] FAST spr round 4 (radius: 25) [05:17:28 -73257.552257] FAST spr round 5 (radius: 25) [05:19:21 -73250.252006] FAST spr round 6 (radius: 25) [05:21:10 -73250.251719] Model parameter optimization (eps = 1.000000) [05:21:24 -73242.445452] SLOW spr round 1 (radius: 5) [05:23:48 -73225.292297] SLOW spr round 2 (radius: 5) [05:26:08 -73223.539412] SLOW spr round 3 (radius: 5) [05:28:26 -73223.539349] SLOW spr round 4 (radius: 10) [05:30:47 -73223.539307] SLOW spr round 5 (radius: 15) [05:34:17 -73223.539266] SLOW spr round 6 (radius: 20) [05:38:41 -73223.264443] SLOW spr round 7 (radius: 5) [05:41:47 -73223.264394] SLOW spr round 8 (radius: 10) [05:44:33 -73223.264351] SLOW spr round 9 (radius: 15) [05:47:52 -73223.264308] SLOW spr round 10 (radius: 20) [05:52:21 -73223.264273] SLOW spr round 11 (radius: 25) [05:57:39 -73222.976197] SLOW spr round 12 (radius: 5) [06:00:47 -73222.975245] SLOW spr round 13 (radius: 10) [06:03:35 -73222.975133] SLOW spr round 14 (radius: 15) [06:06:55 -73222.975087] SLOW spr round 15 (radius: 20) [06:11:22 -73222.975048] SLOW spr round 16 (radius: 25) [06:16:39 -73222.975009] Model parameter optimization (eps = 0.100000) [06:16:45] [worker #0] ML tree search #14, logLikelihood: -73222.963680 [06:16:46 -284580.569001] Initial branch length optimization [06:16:51 -235295.985055] Model parameter optimization (eps = 10.000000) [06:18:00 -233851.385665] AUTODETECT spr round 1 (radius: 5) [06:20:51 -163329.639951] AUTODETECT spr round 2 (radius: 10) [06:23:45 -125154.738430] AUTODETECT spr round 3 (radius: 15) [06:26:50 -103989.387595] AUTODETECT spr round 4 (radius: 20) [06:30:04 -92676.771039] AUTODETECT spr round 5 (radius: 25) [06:33:35 -88352.167179] SPR radius for FAST iterations: 25 (autodetect) [06:33:35 -88352.167179] Model parameter optimization (eps = 3.000000) [06:34:24 -88233.748402] FAST spr round 1 (radius: 25) [06:37:39 -74023.967657] FAST spr round 2 (radius: 25) [06:40:05 -73373.729751] FAST spr round 3 (radius: 25) [06:42:12 -73324.862039] FAST spr round 4 (radius: 25) [06:44:08 -73319.729232] FAST spr round 5 (radius: 25) [06:45:58 -73319.728017] Model parameter optimization (eps = 1.000000) [06:46:19 -73263.094433] SLOW spr round 1 (radius: 5) [06:48:42 -73230.742692] SLOW spr round 2 (radius: 5) [06:49:36] [worker #2] ML tree search #16, logLikelihood: -73214.881224 [06:51:06 -73223.723460] SLOW spr round 3 (radius: 5) [06:53:28 -73223.484537] SLOW spr round 4 (radius: 5) [06:55:47 -73223.484242] SLOW spr round 5 (radius: 10) [06:58:09 -73219.767438] SLOW spr round 6 (radius: 5) [07:01:04 -73217.309692] SLOW spr round 7 (radius: 5) [07:01:10] [worker #1] ML tree search #15, logLikelihood: -73233.128455 [07:03:40 -73216.836347] SLOW spr round 8 (radius: 5) [07:06:12 -73216.276177] SLOW spr round 9 (radius: 5) [07:08:34 -73216.274994] SLOW spr round 10 (radius: 10) [07:10:56 -73216.274878] SLOW spr round 11 (radius: 15) [07:14:29 -73216.274850] SLOW spr round 12 (radius: 20) [07:19:11 -73215.994589] SLOW spr round 13 (radius: 5) [07:22:16 -73215.994066] SLOW spr round 14 (radius: 10) [07:25:02 -73215.994065] SLOW spr round 15 (radius: 15) [07:28:25 -73215.994056] SLOW spr round 16 (radius: 20) [07:33:08 -73215.994055] SLOW spr round 17 (radius: 25) [07:38:55 -73215.994054] Model parameter optimization (eps = 0.100000) [07:39:05] [worker #0] ML tree search #17, logLikelihood: -73215.813870 [07:39:05 -286771.759104] Initial branch length optimization [07:39:11 -237353.976973] Model parameter optimization (eps = 10.000000) [07:39:57 -236069.069635] AUTODETECT spr round 1 (radius: 5) [07:42:45 -167652.399323] AUTODETECT spr round 2 (radius: 10) [07:45:49 -125354.853920] AUTODETECT spr round 3 (radius: 15) [07:48:53 -101292.855087] AUTODETECT spr round 4 (radius: 20) [07:52:15 -91172.962032] AUTODETECT spr round 5 (radius: 25) [07:56:20 -87134.173893] SPR radius for FAST iterations: 25 (autodetect) [07:56:20 -87134.173893] Model parameter optimization (eps = 3.000000) [07:56:58 -86982.552965] FAST spr round 1 (radius: 25) [07:59:55 -73800.258082] FAST spr round 2 (radius: 25) [08:02:10 -73304.394606] FAST spr round 3 (radius: 25) [08:04:17 -73266.344082] FAST spr round 4 (radius: 25) [08:06:12 -73262.697914] FAST spr round 5 (radius: 25) [08:08:02 -73262.467535] FAST spr round 6 (radius: 25) [08:09:51 -73262.466775] Model parameter optimization (eps = 1.000000) [08:10:07 -73259.682312] SLOW spr round 1 (radius: 5) [08:12:30 -73240.395743] SLOW spr round 2 (radius: 5) [08:14:54 -73237.343236] SLOW spr round 3 (radius: 5) [08:16:05] [worker #2] ML tree search #19, logLikelihood: -73227.875493 [08:17:11 -73237.342937] SLOW spr round 4 (radius: 10) [08:19:34 -73234.888439] SLOW spr round 5 (radius: 5) [08:22:30 -73234.127595] SLOW spr round 6 (radius: 5) [08:25:04 -73234.127407] SLOW spr round 7 (radius: 10) [08:27:29 -73234.127376] SLOW spr round 8 (radius: 15) [08:30:46 -73234.127368] SLOW spr round 9 (radius: 20) [08:35:01 -73233.678586] SLOW spr round 10 (radius: 5) [08:38:05 -73233.678583] SLOW spr round 11 (radius: 10) [08:39:22] [worker #1] ML tree search #18, logLikelihood: -73260.719725 [08:40:48 -73233.678581] SLOW spr round 12 (radius: 15) [08:43:59 -73233.678578] SLOW spr round 13 (radius: 20) [08:48:14 -73233.678576] SLOW spr round 14 (radius: 25) [08:53:30 -73233.470278] SLOW spr round 15 (radius: 5) [08:56:34 -73233.468608] SLOW spr round 16 (radius: 10) [08:59:18 -73233.468319] SLOW spr round 17 (radius: 15) [09:02:29 -73233.468259] SLOW spr round 18 (radius: 20) [09:06:44 -73233.468246] SLOW spr round 19 (radius: 25) [09:12:00 -73233.468241] Model parameter optimization (eps = 0.100000) [09:12:10] [worker #0] ML tree search #20, logLikelihood: -73233.327285 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.224584,0.647339) (0.404768,1.155137) (0.322104,0.873584) (0.048544,2.176793) 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: -73191.680965 AIC score: 150337.361931 / AICc score: 7971349.361931 / BIC score: 156477.816133 Free parameters (model + branch lengths): 1977 WARNING: Number of free parameters (K=1977) is larger than alignment size (n=165). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UBH6/3_mltree/Q9UBH6.raxml.log Analysis started: 14-Jul-2021 01:47:49 / finished: 14-Jul-2021 11:00:00 Elapsed time: 33131.093 seconds (this run) / 39019.521 seconds (total with restarts)