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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 07-Jul-2021 17:19:22 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/2_msa/Q12774_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774 --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/Q12774/2_msa/Q12774_trimmed_msa.fasta [00:00:00] Loaded alignment with 698 taxa and 256 sites WARNING: Sequences tr_B4QND4_B4QND4_DROSI_7240 and tr_B4HK96_B4HK96_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NXP9_A0A1D5NXP9_CHICK_9031 and tr_G1MSA1_G1MSA1_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q8BWA8_ARHGJ_MOUSE_10090 and tr_D4A646_D4A646_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XUD8_M3XUD8_MUSPF_9669 and tr_A0A2Y9K390_A0A2Y9K390_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y1N3_M3Y1N3_MUSPF_9669 and tr_A0A2U3VM72_A0A2U3VM72_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y1N3_M3Y1N3_MUSPF_9669 and tr_A0A2Y9IYU8_A0A2Y9IYU8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y1N3_M3Y1N3_MUSPF_9669 and tr_A0A384C1M6_A0A384C1M6_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YXY2_M3YXY2_MUSPF_9669 and tr_A0A2Y9KB74_A0A2Y9KB74_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A2I2Y817_A0A2I2Y817_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and sp_Q96DR7_ARHGQ_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_F7FCL2_F7FCL2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_F6WHA4_F6WHA4_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A0D9RHQ3_A0A0D9RHQ3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A1U7UE36_A0A1U7UE36_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A2K5KJ75_A0A2K5KJ75_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A2K6AZK9_A0A2K6AZK9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A2K6A992_A0A2K6A992_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GQU8_A0A2I3GQU8_NOMLE_61853 and tr_A0A2R9C328_A0A2R9C328_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and tr_G3R8J7_G3R8J7_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and tr_H2NSN5_H2NSN5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and tr_H2R3P8_H2R3P8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and sp_O94989_ARHGF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and tr_A0A0D9RDK1_A0A0D9RDK1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HLS9_A0A2I3HLS9_NOMLE_61853 and tr_A0A2R9AR66_A0A2R9AR66_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NXJ8_G1NXJ8_MYOLU_59463 and tr_F1PGF9_F1PGF9_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1NXJ8_G1NXJ8_MYOLU_59463 and tr_A0A2U3W9R7_A0A2U3W9R7_ODORO_9708 are exactly identical! WARNING: Sequences tr_G3SC71_G3SC71_GORGO_9595 and tr_G3SDL1_G3SDL1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G3SC71_G3SC71_GORGO_9595 and tr_H2QVK1_H2QVK1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SC71_G3SC71_GORGO_9595 and sp_Q12774_ARHG5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5RDX5_NGEF_PONAB_9601 and tr_H2QJM4_H2QJM4_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5RDX5_NGEF_PONAB_9601 and sp_Q8N5V2_NGEF_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5RDX5_NGEF_PONAB_9601 and tr_A0A2R9BK22_A0A2R9BK22_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1TQ06_G1TQ06_RABIT_9986 and tr_F6VCK1_F6VCK1_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A0R3P6T7_A0A0R3P6T7_DROPS_46245 and tr_B4H4E8_B4H4E8_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29E80_Q29E80_DROPS_46245 and tr_B4HAT3_B4HAT3_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2PXV5_H2PXV5_PANTR_9598 and tr_A0A2R8ZRI6_A0A2R8ZRI6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and sp_Q8IW93_ARHGJ_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_F7BQ90_F7BQ90_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_A0A096MVN3_A0A096MVN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_A0A2K5MUY0_A0A2K5MUY0_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_A0A2K6DBT3_A0A2K6DBT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_A0A2K6A4G7_A0A2K6A4G7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PY48_H2PY48_PANTR_9598 and tr_A0A2R9CBJ1_A0A2R9CBJ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5NRT7_W5NRT7_SHEEP_9940 and tr_E1BDY4_E1BDY4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QAP0_W5QAP0_SHEEP_9940 and tr_F1N2G5_F1N2G5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A0R3REP3_A0A0R3REP3_BRUMA_6279 and tr_A0A0N4TLF9_A0A0N4TLF9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0R3REP3_A0A0R3REP3_BRUMA_6279 and tr_A0A0R3QK67_A0A0R3QK67_9BILA_42155 are exactly identical! WARNING: Sequences tr_F6QYC0_F6QYC0_MACMU_9544 and tr_G7P1I7_G7P1I7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QYC0_F6QYC0_MACMU_9544 and tr_A0A096MVW8_A0A096MVW8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QYC0_F6QYC0_MACMU_9544 and tr_A0A0D9R437_A0A0D9R437_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6QYC0_F6QYC0_MACMU_9544 and tr_A0A2K5MGW0_A0A2K5MGW0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QYC0_F6QYC0_MACMU_9544 and tr_A0A2K6DXK0_A0A2K6DXK0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VMG6_F6VMG6_MACMU_9544 and tr_A0A0D9R262_A0A0D9R262_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6VMG6_F6VMG6_MACMU_9544 and tr_A0A2K6CL91_A0A2K6CL91_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DVJ6_F7DVJ6_MACMU_9544 and tr_G7PTK9_G7PTK9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DVJ6_F7DVJ6_MACMU_9544 and tr_A0A096P2U6_A0A096P2U6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DVJ6_F7DVJ6_MACMU_9544 and tr_A0A2K5LSC1_A0A2K5LSC1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DVJ6_F7DVJ6_MACMU_9544 and tr_A0A2K6EBZ1_A0A2K6EBZ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DVJ6_F7DVJ6_MACMU_9544 and tr_A0A2K5Y7W0_A0A2K5Y7W0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZAE5_H0ZAE5_TAEGU_59729 and tr_A0A091E636_A0A091E636_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZAE5_H0ZAE5_TAEGU_59729 and tr_A0A218UCE8_A0A218UCE8_9PASE_299123 are exactly identical! WARNING: Sequences tr_E3MQG7_E3MQG7_CAERE_31234 and tr_A0A261C0M2_A0A261C0M2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_M3VX24_M3VX24_FELCA_9685 and tr_A0A2U3VT66_A0A2U3VT66_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A015L5K5_A0A015L5K5_9GLOM_1432141 and tr_A0A2I1G8G3_A0A2I1G8G3_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015L5K5_A0A015L5K5_9GLOM_1432141 and tr_A0A2H5RJV2_A0A2H5RJV2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044QVY6_A0A044QVY6_ONCVO_6282 and tr_A0A182E9U2_A0A182E9U2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NQQ2_A0A096NQQ2_PAPAN_9555 and tr_A0A2K5NRW8_A0A2K5NRW8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NQQ2_A0A096NQQ2_PAPAN_9555 and tr_A0A2K6AHV1_A0A2K6AHV1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MJ77_A0A151MJ77_ALLMI_8496 and tr_A0A1U8D1S9_A0A1U8D1S9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NBJ8_A0A151NBJ8_ALLMI_8496 and tr_A0A3Q0HF26_A0A3Q0HF26_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NU20_A0A151NU20_ALLMI_8496 and tr_A0A1U7RDF5_A0A1U7RDF5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A183H566_A0A183H566_9BILA_387005 and tr_A0A1I7VTV4_A0A1I7VTV4_LOALO_7209 are exactly identical! WARNING: Sequences tr_A0A091J7B6_A0A091J7B6_EGRGA_188379 and tr_A0A091USN7_A0A091USN7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J7B6_A0A091J7B6_EGRGA_188379 and tr_A0A087RBV6_A0A087RBV6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J7B6_A0A091J7B6_EGRGA_188379 and tr_A0A091X6G4_A0A091X6G4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A087RJS2_A0A087RJS2_APTFO_9233 and tr_A0A093J217_A0A093J217_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A087RJS2_A0A087RJS2_APTFO_9233 and tr_A0A1V4K9T4_A0A1V4K9T4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091GLD0_A0A091GLD0_9AVES_55661 and tr_A0A2I0LTS2_A0A2I0LTS2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091GLD0_A0A091GLD0_9AVES_55661 and tr_A0A1V4K476_A0A1V4K476_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3I9K3_A0A1S3I9K3_LINUN_7574 and tr_A0A2R2ML86_A0A2R2ML86_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1I7T4D6_A0A1I7T4D6_9PELO_1561998 and tr_A0A1I7T4D7_A0A1I7T4D7_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7T4D6_A0A1I7T4D6_9PELO_1561998 and tr_A0A1I7T4D8_A0A1I7T4D8_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226MD29_A0A226MD29_CALSU_9009 and tr_A0A226NUG9_A0A226NUG9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N6M0_A0A226N6M0_CALSU_9009 and tr_A0A226P054_A0A226P054_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NDB2_A0A226NDB2_CALSU_9009 and tr_A0A226PVA1_A0A226PVA1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QAE8_A0A2D0QAE8_ICTPU_7998 and tr_A0A2D0QBJ4_A0A2D0QBJ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QAE8_A0A2D0QAE8_ICTPU_7998 and tr_A0A2D0QBJ8_A0A2D0QBJ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QAE8_A0A2D0QAE8_ICTPU_7998 and tr_A0A2D0QD68_A0A2D0QD68_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S7M6_A0A2D0S7M6_ICTPU_7998 and tr_A0A2D0S8I5_A0A2D0S8I5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S7M6_A0A2D0S7M6_ICTPU_7998 and tr_A0A2D0S937_A0A2D0S937_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5M3X4_A0A2K5M3X4_CERAT_9531 and tr_A0A2K5YV97_A0A2K5YV97_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4B9Q2_A0A2U4B9Q2_TURTR_9739 and tr_A0A2U4B9S8_A0A2U4B9S8_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9NU50_A0A2Y9NU50_DELLE_9749 and tr_A0A2Y9TBK5_A0A2Y9TBK5_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 93 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/Q12774/3_mltree/Q12774.raxml.reduced.phy Alignment comprises 1 partitions and 256 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 256 / 256 Gaps: 6.81 % Invariant sites: 0.39 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.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 698 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 256 / 20480 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -286890.933286] Initial branch length optimization [00:00:05 -240223.339066] Model parameter optimization (eps = 10.000000) [00:00:57 -239984.144299] AUTODETECT spr round 1 (radius: 5) [00:03:01 -148030.204694] AUTODETECT spr round 2 (radius: 10) [00:05:10 -101263.761180] AUTODETECT spr round 3 (radius: 15) [00:07:37 -79895.829571] AUTODETECT spr round 4 (radius: 20) [00:10:39 -73045.394935] AUTODETECT spr round 5 (radius: 25) [00:14:27 -72995.106051] SPR radius for FAST iterations: 25 (autodetect) [00:14:27 -72995.106051] Model parameter optimization (eps = 3.000000) [00:14:51 -72859.701397] FAST spr round 1 (radius: 25) [00:17:14 -63460.616325] FAST spr round 2 (radius: 25) [00:19:08 -63039.769982] FAST spr round 3 (radius: 25) [00:20:41 -63003.741986] FAST spr round 4 (radius: 25) [00:22:03 -63002.574727] FAST spr round 5 (radius: 25) [00:23:23 -63002.574392] Model parameter optimization (eps = 1.000000) [00:23:31 -63001.821431] SLOW spr round 1 (radius: 5) [00:25:28 -62992.381867] SLOW spr round 2 (radius: 5) [00:27:23 -62991.122038] SLOW spr round 3 (radius: 5) [00:29:18 -62990.931340] SLOW spr round 4 (radius: 5) [00:31:08 -62990.931129] SLOW spr round 5 (radius: 10) [00:33:01 -62988.228076] SLOW spr round 6 (radius: 5) [00:35:26 -62988.227784] SLOW spr round 7 (radius: 10) [00:37:36 -62988.227703] SLOW spr round 8 (radius: 15) [00:40:34 -62988.193954] SLOW spr round 9 (radius: 20) [00:45:06 -62988.193937] SLOW spr round 10 (radius: 25) [00:51:08 -62988.193923] Model parameter optimization (eps = 0.100000) [00:51:13] [worker #0] ML tree search #1, logLikelihood: -62988.182426 [00:51:13 -287430.314811] Initial branch length optimization [00:51:17 -240017.771401] Model parameter optimization (eps = 10.000000) [00:51:59 -239678.039262] AUTODETECT spr round 1 (radius: 5) [00:54:01 -146297.919750] AUTODETECT spr round 2 (radius: 10) [00:56:12 -103281.295338] AUTODETECT spr round 3 (radius: 15) [00:56:55] [worker #1] ML tree search #2, logLikelihood: -62990.977156 [00:58:35 -86307.963225] AUTODETECT spr round 4 (radius: 20) [01:01:10 -80912.531903] AUTODETECT spr round 5 (radius: 25) [01:01:54] [worker #2] ML tree search #3, logLikelihood: -62980.526878 [01:03:11] [worker #3] ML tree search #4, logLikelihood: -62971.839998 [01:04:25 -76825.006767] SPR radius for FAST iterations: 25 (autodetect) [01:04:25 -76825.006767] Model parameter optimization (eps = 3.000000) [01:04:52 -76713.036781] FAST spr round 1 (radius: 25) [01:07:07 -63929.497377] FAST spr round 2 (radius: 25) [01:09:01 -63071.988520] FAST spr round 3 (radius: 25) [01:10:38 -63027.730678] FAST spr round 4 (radius: 25) [01:12:05 -63021.962494] FAST spr round 5 (radius: 25) [01:13:29 -63017.751408] FAST spr round 6 (radius: 25) [01:14:49 -63017.751378] Model parameter optimization (eps = 1.000000) [01:15:04 -63014.038427] SLOW spr round 1 (radius: 5) [01:17:00 -62995.534566] SLOW spr round 2 (radius: 5) [01:18:58 -62990.931115] SLOW spr round 3 (radius: 5) [01:20:35] [worker #4] ML tree search #5, logLikelihood: -62977.319905 [01:20:57 -62990.357030] SLOW spr round 4 (radius: 5) [01:22:48 -62990.356972] SLOW spr round 5 (radius: 10) [01:24:47 -62984.489031] SLOW spr round 6 (radius: 5) [01:27:16 -62984.488983] SLOW spr round 7 (radius: 10) [01:29:31 -62984.488983] SLOW spr round 8 (radius: 15) [01:32:34 -62984.056341] SLOW spr round 9 (radius: 5) [01:35:11 -62984.056335] SLOW spr round 10 (radius: 10) [01:37:34 -62984.056335] SLOW spr round 11 (radius: 15) [01:40:36 -62984.056335] SLOW spr round 12 (radius: 20) [01:45:13 -62983.832609] SLOW spr round 13 (radius: 5) [01:47:02] [worker #1] ML tree search #7, logLikelihood: -62977.638817 [01:47:52 -62983.831546] SLOW spr round 14 (radius: 10) [01:50:20 -62983.831317] SLOW spr round 15 (radius: 15) [01:53:18 -62983.831281] SLOW spr round 16 (radius: 20) [01:53:20] [worker #3] ML tree search #9, logLikelihood: -62991.415165 [01:57:52 -62983.831276] SLOW spr round 17 (radius: 25) [02:03:46 -62983.831276] Model parameter optimization (eps = 0.100000) [02:04:00] [worker #0] ML tree search #6, logLikelihood: -62983.561431 [02:04:00 -288584.532086] Initial branch length optimization [02:04:05 -241730.259077] Model parameter optimization (eps = 10.000000) [02:04:48 -241527.731998] AUTODETECT spr round 1 (radius: 5) [02:05:07] [worker #2] ML tree search #8, logLikelihood: -62990.137411 [02:06:53 -146387.842582] AUTODETECT spr round 2 (radius: 10) [02:09:04 -100117.986620] AUTODETECT spr round 3 (radius: 15) [02:11:28 -87450.509364] AUTODETECT spr round 4 (radius: 20) [02:12:40] [worker #4] ML tree search #10, logLikelihood: -62974.188121 [02:14:31 -74806.256734] AUTODETECT spr round 5 (radius: 25) [02:18:21 -73730.063126] SPR radius for FAST iterations: 25 (autodetect) [02:18:21 -73730.063126] Model parameter optimization (eps = 3.000000) [02:18:54 -73581.862495] FAST spr round 1 (radius: 25) [02:21:13 -63840.818499] FAST spr round 2 (radius: 25) [02:22:58 -63112.186687] FAST spr round 3 (radius: 25) [02:24:33 -63032.741704] FAST spr round 4 (radius: 25) [02:25:58 -63024.148593] FAST spr round 5 (radius: 25) [02:27:16 -63024.147737] Model parameter optimization (eps = 1.000000) [02:27:31 -63022.787167] SLOW spr round 1 (radius: 5) [02:29:27 -63006.056484] SLOW spr round 2 (radius: 5) [02:31:24 -63004.983438] SLOW spr round 3 (radius: 5) [02:33:20 -63004.827021] SLOW spr round 4 (radius: 5) [02:35:13 -63004.826955] SLOW spr round 5 (radius: 10) [02:37:11 -63003.496577] SLOW spr round 6 (radius: 5) [02:38:52] [worker #3] ML tree search #14, logLikelihood: -62979.932804 [02:39:26] [worker #1] ML tree search #12, logLikelihood: -62991.530168 [02:39:40 -63003.496511] SLOW spr round 7 (radius: 10) [02:41:56 -63003.496509] SLOW spr round 8 (radius: 15) [02:44:58 -63003.076441] SLOW spr round 9 (radius: 5) [02:47:34 -63003.076437] SLOW spr round 10 (radius: 10) [02:50:01 -63000.433091] SLOW spr round 11 (radius: 5) [02:52:26 -62997.341369] SLOW spr round 12 (radius: 5) [02:54:33 -62993.470825] SLOW spr round 13 (radius: 5) [02:56:31 -62993.470654] SLOW spr round 14 (radius: 10) [02:58:28 -62993.470654] SLOW spr round 15 (radius: 15) [03:01:39 -62993.470654] SLOW spr round 16 (radius: 20) [03:06:13 -62993.470654] SLOW spr round 17 (radius: 25) [03:07:44] [worker #2] ML tree search #13, logLikelihood: -62981.364073 [03:12:25 -62993.470654] Model parameter optimization (eps = 0.100000) [03:12:36] [worker #0] ML tree search #11, logLikelihood: -62993.269461 [03:12:36 -287674.905306] Initial branch length optimization [03:12:42 -239021.378804] Model parameter optimization (eps = 10.000000) [03:13:23 -238762.347022] AUTODETECT spr round 1 (radius: 5) [03:15:28 -144659.008791] AUTODETECT spr round 2 (radius: 10) [03:17:36 -103565.750920] AUTODETECT spr round 3 (radius: 15) [03:20:00 -85707.164937] AUTODETECT spr round 4 (radius: 20) [03:21:14] [worker #4] ML tree search #15, logLikelihood: -62981.689294 [03:23:15 -75099.458260] AUTODETECT spr round 5 (radius: 25) [03:27:27 -73612.669387] SPR radius for FAST iterations: 25 (autodetect) [03:27:27 -73612.669387] Model parameter optimization (eps = 3.000000) [03:27:56 -73513.343309] FAST spr round 1 (radius: 25) [03:28:40] [worker #3] ML tree search #19, logLikelihood: -63002.340085 [03:30:21 -63410.121215] FAST spr round 2 (radius: 25) [03:32:17 -63048.809236] FAST spr round 3 (radius: 25) [03:33:50 -63038.759835] FAST spr round 4 (radius: 25) [03:35:12 -63038.670195] Model parameter optimization (eps = 1.000000) [03:35:31 -63033.451047] SLOW spr round 1 (radius: 5) [03:37:31 -63016.604954] SLOW spr round 2 (radius: 5) [03:37:57] [worker #1] ML tree search #17, logLikelihood: -62980.808698 [03:39:31 -63011.129728] SLOW spr round 3 (radius: 5) [03:41:29 -63010.910887] SLOW spr round 4 (radius: 5) [03:43:20 -63010.910371] SLOW spr round 5 (radius: 10) [03:45:14 -63009.551759] SLOW spr round 6 (radius: 5) [03:47:40 -63009.551192] SLOW spr round 7 (radius: 10) [03:49:53 -63009.551026] SLOW spr round 8 (radius: 15) [03:52:52 -63009.550906] SLOW spr round 9 (radius: 20) [03:57:25 -63009.312725] SLOW spr round 10 (radius: 5) [04:00:02 -63009.312122] SLOW spr round 11 (radius: 10) [04:02:28 -63009.312019] SLOW spr round 12 (radius: 15) [04:05:21 -63009.311972] SLOW spr round 13 (radius: 20) [04:09:52 -63009.311940] SLOW spr round 14 (radius: 25) [04:15:51 -63009.311915] Model parameter optimization (eps = 0.100000) [04:16:02] [worker #0] ML tree search #16, logLikelihood: -63009.065739 [04:18:22] [worker #2] ML tree search #18, logLikelihood: -62986.826126 [04:49:17] [worker #4] ML tree search #20, logLikelihood: -62988.110361 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.203289,0.448913) (0.235611,0.528094) (0.331743,0.873754) (0.229356,2.155833) 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: -62971.839998 AIC score: 128741.679995 / AICc score: 4045941.679995 / BIC score: 133701.383240 Free parameters (model + branch lengths): 1399 WARNING: Number of free parameters (K=1399) is larger than alignment size (n=256). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 164 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12774/3_mltree/Q12774.raxml.log Analysis started: 07-Jul-2021 17:19:22 / finished: 07-Jul-2021 22:08:40 Elapsed time: 17358.040 seconds Consumed energy: 1168.979 Wh (= 6 km in an electric car, or 29 km with an e-scooter!)