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 01-Jul-2021 11:25:14 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/2_msa/Q7Z3J3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/3_mltree/Q7Z3J3 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/2_msa/Q7Z3J3_trimmed_msa.fasta [00:00:00] Loaded alignment with 987 taxa and 234 sites WARNING: Sequences tr_Q5ZJ38_Q5ZJ38_CHICK_9031 and tr_A0A226N8Z5_A0A226N8Z5_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q5ZJ38_Q5ZJ38_CHICK_9031 and tr_A0A226PYA8_A0A226PYA8_COLVI_9014 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2I3SUC0_A0A2I3SUC0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A1D5RHC9_A0A1D5RHC9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2I3M5Z7_A0A2I3M5Z7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2K5M2D6_A0A2K5M2D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2K6BKU9_A0A2K6BKU9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2K5ZMS6_A0A2K5ZMS6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R119_G1R119_NOMLE_61853 and tr_A0A2R9CFI6_A0A2R9CFI6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E1RVV2_A0A0E1RVV2_COCIM_246410 and tr_E9D2I8_E9D2I8_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1RVV2_A0A0E1RVV2_COCIM_246410 and tr_A0A0J7BF99_A0A0J7BF99_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q9R4_B6Q9R4_TALMQ_441960 and tr_A0A093XM08_A0A093XM08_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WJ58_B2WJ58_PYRTR_426418 and tr_A0A2W1D5I8_A0A2W1D5I8_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3R6A2_G3R6A2_GORGO_9595 and tr_A0A2K6HGX5_A0A2K6HGX5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6A2_G3R6A2_GORGO_9595 and tr_H3A5C5_H3A5C5_LATCH_7897 are exactly identical! WARNING: Sequences tr_G3R6A2_G3R6A2_GORGO_9595 and tr_A0A2I2UZY4_A0A2I2UZY4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G3R6A2_G3R6A2_GORGO_9595 and tr_A0A2R9A2X4_A0A2R9A2X4_PANPA_9597 are exactly identical! WARNING: Sequences tr_C3ZEZ0_C3ZEZ0_BRAFL_7739 and tr_C3ZQV8_C3ZQV8_BRAFL_7739 are exactly identical! WARNING: Sequences tr_A0A2J8RBQ5_A0A2J8RBQ5_PONAB_9601 and sp_P43487_RANG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8RBQ5_A0A2J8RBQ5_PONAB_9601 and tr_A0A0D9RHX8_A0A0D9RHX8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_U9W553_U9W553_NEUCR_367110 and tr_G4UP01_G4UP01_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A179UWG1_A0A179UWG1_BLAGS_559298 and tr_C5GLI9_C5GLI9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9G4U0_F9G4U0_FUSOF_660025 and tr_A0A0D2Y5H4_A0A0D2Y5H4_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G4U0_F9G4U0_FUSOF_660025 and tr_S0EIG4_S0EIG4_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9G4U0_F9G4U0_FUSOF_660025 and tr_N4UH46_N4UH46_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G4U0_F9G4U0_FUSOF_660025 and tr_X0D6D7_X0D6D7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G4U0_F9G4U0_FUSOF_660025 and tr_A0A365NHL3_A0A365NHL3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9ER24_E9ER24_METRA_655844 and tr_A0A0B4HQA4_A0A0B4HQA4_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9ER24_E9ER24_METRA_655844 and tr_A0A0D9PGX9_A0A0D9PGX9_METAN_1291518 are exactly identical! WARNING: Sequences tr_J5JQ07_J5JQ07_BEAB2_655819 and tr_A0A0A2VVF9_A0A0A2VVF9_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JQ07_J5JQ07_BEAB2_655819 and tr_A0A2N6NCC0_A0A2N6NCC0_BEABA_176275 are exactly identical! WARNING: Sequences sp_O14715_RGPD8_HUMAN_9606 and sp_Q99666_RGPD5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P0DJD0_RGPD1_HUMAN_9606 and sp_P0DJD1_RGPD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q2U689_Q2U689_ASPOR_510516 and tr_A0A1S9D8K8_A0A1S9D8K8_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A2RA71_A2RA71_ASPNC_425011 and tr_G3YDM7_G3YDM7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_F6UF21_F6UF21_MACMU_9544 and tr_G7PMX0_G7PMX0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HI99_F7HI99_MACMU_9544 and tr_G7PMX2_G7PMX2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HI99_F7HI99_MACMU_9544 and tr_A0A2K6E1L3_A0A2K6E1L3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X9P7_G7X9P7_ASPKW_1033177 and tr_A0A146F6N6_A0A146F6N6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_W4YG72_W4YG72_STRPU_7668 and tr_W4YVI0_W4YVI0_STRPU_7668 are exactly identical! WARNING: Sequences tr_F4P0Q8_F4P0Q8_BATDJ_684364 and tr_A0A177WD68_A0A177WD68_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9X2P5_F9X2P5_ZYMTI_336722 and tr_A0A1X7RIY2_A0A1X7RIY2_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XNM3_G2XNM3_BOTF4_999810 and tr_M7TPS9_M7TPS9_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_D4AJE7_D4AJE7_ARTBC_663331 and tr_F2PUN2_F2PUN2_TRIEC_559882 are exactly identical! WARNING: Sequences tr_D4AJE7_D4AJE7_ARTBC_663331 and tr_A0A059IZ14_A0A059IZ14_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0PE37_L0PE37_PNEJ8_1209962 and tr_A0A0W4ZW58_A0A0W4ZW58_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M3WXW5_M3WXW5_FELCA_9685 and tr_A0A2R9CLK1_A0A2R9CLK1_PANPA_9597 are exactly identical! WARNING: Sequences tr_U5H9P1_U5H9P1_USTV1_683840 and tr_A0A2X0LRN9_A0A2X0LRN9_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XXC0_V2XXC0_MONRO_1381753 and tr_A0A0W0F8R5_A0A0W0F8R5_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015IGS6_A0A015IGS6_9GLOM_1432141 and tr_A0A2H5RM43_A0A2H5RM43_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NCD4_A0A096NCD4_PAPAN_9555 and tr_A0A2K6B0Z2_A0A2K6B0Z2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A094HA21_A0A094HA21_9PEZI_1420912 and tr_A0A1B8GWB9_A0A1B8GWB9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F0IRN8_A0A0F0IRN8_ASPPU_1403190 and tr_A0A2G7G9J1_A0A2G7G9J1_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A091VQF2_A0A091VQF2_NIPNI_128390 and tr_A0A087QSM3_A0A087QSM3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VQI4_A0A091VQI4_NIPNI_128390 and tr_A0A091FTV3_A0A091FTV3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093H2T5_A0A093H2T5_STRCA_441894 and tr_A0A091FTL8_A0A091FTL8_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093H2T5_A0A093H2T5_STRCA_441894 and tr_A0A091IGM9_A0A091IGM9_CALAN_9244 are exactly identical! WARNING: Sequences tr_W6YPC5_W6YPC5_COCCA_930089 and tr_W6ZGZ6_W6ZGZ6_COCMI_930090 are exactly identical! WARNING: Sequences tr_A0A0V1CIE8_A0A0V1CIE8_TRIBR_45882 and tr_A0A0V1P6X9_A0A0V1P6X9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0VRB3_A0A0V0VRB3_9BILA_181606 and tr_A0A0V0TGR9_A0A0V0TGR9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4BYR1_A0A1S4BYR1_TOBAC_4097 and tr_A0A1U7XSD8_A0A1U7XSD8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3NYT1_A0A1S3NYT1_SALSA_8030 and tr_A0A1S3NYW4_A0A1S3NYW4_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3NYY3_A0A1S3NYY3_SALSA_8030 and tr_A0A1S3NZ19_A0A1S3NZ19_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1V8U106_A0A1V8U106_9PEZI_1974281 and tr_A0A1V8TGD1_A0A1V8TGD1_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A226M7R8_A0A226M7R8_CALSU_9009 and tr_A0A226M7Z2_A0A226M7Z2_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A226M7R8_A0A226M7R8_CALSU_9009 and tr_A0A226MC13_A0A226MC13_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A2H3F7X4_A0A2H3F7X4_9HELO_946125 and tr_A0A218ZHJ1_A0A218ZHJ1_9HELO_503106 are exactly identical! WARNING: Sequences tr_A0A1U8E398_A0A1U8E398_CAPAN_4072 and tr_A0A2G3BSF8_A0A2G3BSF8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G5I3G4_A0A2G5I3G4_CERBT_122368 and tr_A0A2S6C6D3_A0A2S6C6D3_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2S7NU48_A0A2S7NU48_9HELO_2070414 and tr_A0A2S7QU84_A0A2S7QU84_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2U4B194_A0A2U4B194_TURTR_9739 and tr_A0A2Y9QBP6_A0A2Y9QBP6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B194_A0A2U4B194_TURTR_9739 and tr_A0A2Y9S809_A0A2Y9S809_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VT13_A0A2U3VT13_ODORO_9708 and tr_A0A2U3XBZ4_A0A2U3XBZ4_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 73 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/Q7Z3J3/3_mltree/Q7Z3J3.raxml.reduced.phy Alignment comprises 1 partitions and 234 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 234 / 234 Gaps: 19.90 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/3_mltree/Q7Z3J3.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 987 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 234 / 18720 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -310462.496423] Initial branch length optimization [00:00:05 -259795.669894] Model parameter optimization (eps = 10.000000) [00:01:26 -259068.913067] AUTODETECT spr round 1 (radius: 5) [00:04:23 -186706.762031] AUTODETECT spr round 2 (radius: 10) [00:07:30 -143328.435300] AUTODETECT spr round 3 (radius: 15) [00:11:08 -117864.828770] AUTODETECT spr round 4 (radius: 20) [00:15:01 -108353.015449] AUTODETECT spr round 5 (radius: 25) [00:19:25 -104259.045535] SPR radius for FAST iterations: 25 (autodetect) [00:19:25 -104259.045535] Model parameter optimization (eps = 3.000000) [00:20:01 -104221.817255] FAST spr round 1 (radius: 25) [00:23:58 -91216.081744] FAST spr round 2 (radius: 25) [00:26:54 -90550.534050] FAST spr round 3 (radius: 25) [00:29:21 -90505.667298] FAST spr round 4 (radius: 25) [00:31:34 -90498.223435] FAST spr round 5 (radius: 25) [00:33:35 -90498.164495] Model parameter optimization (eps = 1.000000) [00:33:49 -90495.992972] SLOW spr round 1 (radius: 5) [00:36:35 -90468.294765] SLOW spr round 2 (radius: 5) [00:39:06 -90466.959415] SLOW spr round 3 (radius: 5) [00:41:29 -90466.956490] SLOW spr round 4 (radius: 10) [00:43:57 -90463.583608] SLOW spr round 5 (radius: 5) [00:47:10 -90457.497654] SLOW spr round 6 (radius: 5) [00:49:54 -90457.485628] SLOW spr round 7 (radius: 10) [00:52:26 -90455.150607] SLOW spr round 8 (radius: 5) [00:55:34 -90453.310738] SLOW spr round 9 (radius: 5) [00:58:15 -90453.309669] SLOW spr round 10 (radius: 10) [01:00:46 -90453.309196] SLOW spr round 11 (radius: 15) [01:04:50 -90453.230662] SLOW spr round 12 (radius: 20) [01:10:56 -90453.153788] SLOW spr round 13 (radius: 25) [01:19:11 -90453.144548] Model parameter optimization (eps = 0.100000) [01:19:20] [worker #0] ML tree search #1, logLikelihood: -90452.064357 [01:19:21 -308997.322330] Initial branch length optimization [01:19:25 -259121.811853] Model parameter optimization (eps = 10.000000) [01:21:20 -258198.325565] AUTODETECT spr round 1 (radius: 5) [01:24:07 -190236.583607] AUTODETECT spr round 2 (radius: 10) [01:25:42] [worker #2] ML tree search #3, logLikelihood: -90730.536043 [01:27:06 -147892.871486] AUTODETECT spr round 3 (radius: 15) [01:30:24 -121524.995728] AUTODETECT spr round 4 (radius: 20) [01:32:26] [worker #1] ML tree search #2, logLikelihood: -90495.995050 [01:34:11 -114672.073877] AUTODETECT spr round 5 (radius: 25) [01:38:28 -108229.763941] SPR radius for FAST iterations: 25 (autodetect) [01:38:28 -108229.763941] Model parameter optimization (eps = 3.000000) [01:38:56 -108171.278085] FAST spr round 1 (radius: 25) [01:42:47 -93345.083127] FAST spr round 2 (radius: 25) [01:45:29 -91527.790946] FAST spr round 3 (radius: 25) [01:47:48 -90606.900784] FAST spr round 4 (radius: 25) [01:49:51 -90561.046769] FAST spr round 5 (radius: 25) [01:51:46 -90552.794365] FAST spr round 6 (radius: 25) [01:53:35 -90549.033437] FAST spr round 7 (radius: 25) [01:55:22 -90549.033142] Model parameter optimization (eps = 1.000000) [01:55:55 -90540.985681] SLOW spr round 1 (radius: 5) [01:58:23 -90517.347978] SLOW spr round 2 (radius: 5) [02:00:53 -90513.052327] SLOW spr round 3 (radius: 5) [02:03:18 -90511.216292] SLOW spr round 4 (radius: 5) [02:04:58] [worker #3] ML tree search #4, logLikelihood: -92663.478229 [02:05:40 -90511.215953] SLOW spr round 5 (radius: 10) [02:08:04 -90511.036675] SLOW spr round 6 (radius: 5) [02:11:10 -90511.035550] SLOW spr round 7 (radius: 10) [02:13:52 -90511.035328] SLOW spr round 8 (radius: 15) [02:17:18] [worker #4] ML tree search #5, logLikelihood: -90499.530900 [02:17:39 -90510.009624] SLOW spr round 9 (radius: 5) [02:20:53 -90510.007523] SLOW spr round 10 (radius: 10) [02:23:42 -90510.006462] SLOW spr round 11 (radius: 15) [02:27:26 -90510.005768] SLOW spr round 12 (radius: 20) [02:32:54 -90510.005288] SLOW spr round 13 (radius: 25) [02:39:42 -90510.004943] Model parameter optimization (eps = 0.100000) [02:39:47] [worker #0] ML tree search #6, logLikelihood: -90509.977263 [02:39:48 -311288.974707] Initial branch length optimization [02:39:52 -260266.417193] Model parameter optimization (eps = 10.000000) [02:41:34 -259258.931779] AUTODETECT spr round 1 (radius: 5) [02:44:23 -187503.332889] AUTODETECT spr round 2 (radius: 10) [02:47:22 -141537.879916] AUTODETECT spr round 3 (radius: 15) [02:50:36 -116605.533706] AUTODETECT spr round 4 (radius: 20) [02:54:50 -111625.240790] AUTODETECT spr round 5 (radius: 25) [02:58:06] [worker #1] ML tree search #7, logLikelihood: -90610.635857 [02:59:49 -106417.715464] SPR radius for FAST iterations: 25 (autodetect) [02:59:49 -106417.715464] Model parameter optimization (eps = 3.000000) [03:00:17 -106361.489246] FAST spr round 1 (radius: 25) [03:04:06 -93308.716057] FAST spr round 2 (radius: 25) [03:06:56 -90847.928531] FAST spr round 3 (radius: 25) [03:09:17 -90530.969581] FAST spr round 4 (radius: 25) [03:11:24 -90517.769471] FAST spr round 5 (radius: 25) [03:13:19 -90516.368288] FAST spr round 6 (radius: 25) [03:15:11 -90514.805911] FAST spr round 7 (radius: 25) [03:16:59 -90514.805804] Model parameter optimization (eps = 1.000000) [03:17:17 -90505.313704] SLOW spr round 1 (radius: 5) [03:19:53 -90471.349908] SLOW spr round 2 (radius: 5) [03:21:23] [worker #3] ML tree search #9, logLikelihood: -90486.019376 [03:22:24 -90464.744346] SLOW spr round 3 (radius: 5) [03:24:51 -90462.617789] SLOW spr round 4 (radius: 5) [03:27:15 -90462.617591] SLOW spr round 5 (radius: 10) [03:29:41 -90461.407158] SLOW spr round 6 (radius: 5) [03:32:47 -90461.406990] SLOW spr round 7 (radius: 10) [03:35:30 -90461.406863] SLOW spr round 8 (radius: 15) [03:39:18 -90460.248889] SLOW spr round 9 (radius: 5) [03:42:13] [worker #2] ML tree search #8, logLikelihood: -90478.917989 [03:42:32 -90460.246076] SLOW spr round 10 (radius: 10) [03:45:24 -90460.244508] SLOW spr round 11 (radius: 15) [03:49:08 -90460.243583] SLOW spr round 12 (radius: 20) [03:54:57 -90459.568057] SLOW spr round 13 (radius: 5) [03:57:45] [worker #4] ML tree search #10, logLikelihood: -90490.681063 [03:58:16 -90459.478438] SLOW spr round 14 (radius: 10) [04:01:16 -90459.476758] SLOW spr round 15 (radius: 15) [04:05:05 -90459.476262] SLOW spr round 16 (radius: 20) [04:11:04 -90459.476117] SLOW spr round 17 (radius: 25) [04:11:11] [worker #1] ML tree search #12, logLikelihood: -90474.421003 [04:19:05 -90459.476074] Model parameter optimization (eps = 0.100000) [04:19:10] [worker #0] ML tree search #11, logLikelihood: -90459.459354 [04:19:10 -312376.872924] Initial branch length optimization [04:19:15 -261397.615772] Model parameter optimization (eps = 10.000000) [04:20:45 -260451.422654] AUTODETECT spr round 1 (radius: 5) [04:23:34 -189710.457453] AUTODETECT spr round 2 (radius: 10) [04:26:31 -143608.463971] AUTODETECT spr round 3 (radius: 15) [04:29:45 -124499.559287] AUTODETECT spr round 4 (radius: 20) [04:33:33 -109872.813233] AUTODETECT spr round 5 (radius: 25) [04:37:48 -106421.136141] SPR radius for FAST iterations: 25 (autodetect) [04:37:48 -106421.136141] Model parameter optimization (eps = 3.000000) [04:38:16 -106378.954011] FAST spr round 1 (radius: 25) [04:42:16 -93609.290668] FAST spr round 2 (radius: 25) [04:42:28] [worker #3] ML tree search #14, logLikelihood: -90499.458440 [04:44:59 -91053.175406] FAST spr round 3 (radius: 25) [04:47:16 -90545.536087] FAST spr round 4 (radius: 25) [04:49:21 -90520.110674] FAST spr round 5 (radius: 25) [04:51:16 -90516.697780] FAST spr round 6 (radius: 25) [04:53:06 -90516.688376] Model parameter optimization (eps = 1.000000) [04:53:19 -90515.064011] SLOW spr round 1 (radius: 5) [04:55:52 -90487.283313] SLOW spr round 2 (radius: 5) [04:58:23 -90484.555643] SLOW spr round 3 (radius: 5) [05:00:47 -90484.555550] SLOW spr round 4 (radius: 10) [05:03:14 -90484.102879] SLOW spr round 5 (radius: 5) [05:06:19 -90484.102699] SLOW spr round 6 (radius: 10) [05:09:03 -90484.102649] SLOW spr round 7 (radius: 15) [05:12:50 -90483.664104] SLOW spr round 8 (radius: 5) [05:15:40] [worker #2] ML tree search #13, logLikelihood: -90503.556055 [05:16:06 -90483.539844] SLOW spr round 9 (radius: 5) [05:18:55 -90483.526441] SLOW spr round 10 (radius: 10) [05:21:30 -90483.526351] SLOW spr round 11 (radius: 15) [05:21:48] [worker #4] ML tree search #15, logLikelihood: -90469.296991 [05:25:21 -90483.526278] SLOW spr round 12 (radius: 20) [05:30:51 -90483.157194] SLOW spr round 13 (radius: 5) [05:32:00] [worker #1] ML tree search #17, logLikelihood: -90490.878638 [05:34:08 -90483.155025] SLOW spr round 14 (radius: 10) [05:37:04 -90483.154187] SLOW spr round 15 (radius: 15) [05:40:45 -90483.153781] SLOW spr round 16 (radius: 20) [05:46:18 -90483.058303] SLOW spr round 17 (radius: 25) [05:53:24 -90483.033649] Model parameter optimization (eps = 0.100000) [05:53:29] [worker #0] ML tree search #16, logLikelihood: -90483.008997 [06:29:01] [worker #3] ML tree search #19, logLikelihood: -90458.474469 [07:02:06] [worker #4] ML tree search #20, logLikelihood: -90607.767222 [07:16:43] [worker #2] ML tree search #18, logLikelihood: -92825.720638 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.134646,0.193476) (0.160967,0.351312) (0.243244,0.610639) (0.461143,1.667304) 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: -90452.064357 AIC score: 184858.128715 / AICc score: 8005870.128715 / BIC score: 191689.298560 Free parameters (model + branch lengths): 1977 WARNING: Number of free parameters (K=1977) is larger than alignment size (n=234). 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/Q7Z3J3/3_mltree/Q7Z3J3.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/3_mltree/Q7Z3J3.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/3_mltree/Q7Z3J3.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3J3/3_mltree/Q7Z3J3.raxml.log Analysis started: 01-Jul-2021 11:25:14 / finished: 01-Jul-2021 18:41:57 Elapsed time: 26203.283 seconds Consumed energy: 1772.798 Wh (= 9 km in an electric car, or 44 km with an e-scooter!)