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 20:25:00 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/2_msa/Q96P64_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/3_mltree/Q96P64 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/2_msa/Q96P64_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 525 sites WARNING: Sequences tr_B4R1D5_B4R1D5_DROSI_7240 and tr_Q9VCQ6_Q9VCQ6_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5PI31_A0A1D5PI31_CHICK_9031 and tr_A0A226MW26_A0A226MW26_CALSU_9009 are exactly identical! WARNING: Sequences tr_M3XQM3_M3XQM3_MUSPF_9669 and tr_A0A2Y9JB63_A0A2Y9JB63_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XXB2_M3XXB2_MUSPF_9669 and tr_G1LS46_G1LS46_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXB2_M3XXB2_MUSPF_9669 and tr_A0A2U3VBN3_A0A2U3VBN3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XXB2_M3XXB2_MUSPF_9669 and tr_A0A2Y9KBY1_A0A2Y9KBY1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_H2QP05_H2QP05_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and sp_Q15057_ACAP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GNP3_A0A2I3GNP3_NOMLE_61853 and tr_A0A2R9BJT9_A0A2R9BJT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HAK8_A0A2I3HAK8_NOMLE_61853 and tr_G3R222_G3R222_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HAK8_A0A2I3HAK8_NOMLE_61853 and tr_A0A2I3SFN4_A0A2I3SFN4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HAK8_A0A2I3HAK8_NOMLE_61853 and tr_A0A2R8ZI72_A0A2R8ZI72_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_K7CJ94_K7CJ94_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and sp_Q8N7R7_CCYL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_F7HYI9_F7HYI9_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A096MLE9_A0A096MLE9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A0D9RCH8_A0A0D9RCH8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A2K5MQH6_A0A2K5MQH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A2K6CK18_A0A2K6CK18_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A2K6A287_A0A2K6A287_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2Y7M7_A0A2I2Y7M7_GORGO_9595 and tr_A0A2R9B0L8_A0A2R9B0L8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PP27_H2PP27_PONAB_9601 and tr_H2QVM6_H2QVM6_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PP27_H2PP27_PONAB_9601 and sp_Q96P47_AGAP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PP27_H2PP27_PONAB_9601 and tr_A0A2R9A9E7_A0A2R9A9E7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0R3NEV5_A0A0R3NEV5_DROPS_46245 and tr_B4GP69_B4GP69_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_F7BFQ7_F7BFQ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_F7HRE7_F7HRE7_CALJA_9483 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_A0A0D9S392_A0A0D9S392_CHLSB_60711 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_A0A2U3ZWW1_A0A2U3ZWW1_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_A0A2U3Y2C9_A0A2U3Y2C9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2R8Q3_E2R8Q3_CANLF_9615 and tr_A0A2Y9KNH9_A0A2Y9KNH9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2RD06_H2RD06_PANTR_9598 and tr_A0A2R9BF19_A0A2R9BF19_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PXZ1_W5PXZ1_SHEEP_9940 and tr_E1BI41_E1BI41_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QGQ4_W5QGQ4_SHEEP_9940 and tr_F1MZ03_F1MZ03_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158NGM0_A0A158NGM0_ATTCE_12957 and tr_A0A195B7V5_A0A195B7V5_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5QZQ4_A0A1D5QZQ4_MACMU_9544 and tr_G7P219_G7P219_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QZQ4_A0A1D5QZQ4_MACMU_9544 and tr_A0A2K5MPF4_A0A2K5MPF4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QZQ4_A0A1D5QZQ4_MACMU_9544 and tr_A0A2K6CGD5_A0A2K6CGD5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R919_A0A1D5R919_MACMU_9544 and tr_G7NYR9_G7NYR9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R919_A0A1D5R919_MACMU_9544 and tr_A0A2I3NCN3_A0A2I3NCN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R919_A0A1D5R919_MACMU_9544 and tr_A0A2K5MSE0_A0A2K5MSE0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R919_A0A1D5R919_MACMU_9544 and tr_A0A2K6DUQ0_A0A2K6DUQ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R919_A0A1D5R919_MACMU_9544 and tr_A0A2K5Y267_A0A2K5Y267_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A096NYF0_A0A096NYF0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A0D9QX81_A0A0D9QX81_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A2K5KRJ1_A0A2K5KRJ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HCY1_F7HCY1_MACMU_9544 and tr_A0A2K6E4Y1_A0A2K6E4Y1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A096N8D9_A0A096N8D9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A2K5LEQ3_A0A2K5LEQ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HJG6_F7HJG6_MACMU_9544 and tr_A0A2K6BBK1_A0A2K6BBK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HLN4_F7HLN4_MACMU_9544 and tr_A0A2K6BQW9_A0A2K6BQW9_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9FTD4_H9FTD4_MACMU_9544 and tr_A0A2I3N014_A0A2I3N014_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9FTD4_H9FTD4_MACMU_9544 and tr_A0A2K5LK29_A0A2K5LK29_CERAT_9531 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_E5SZN3_E5SZN3_TRISP_6334 are exactly identical! WARNING: Sequences tr_E5RZD8_E5RZD8_TRISP_6334 and tr_A0A0V0RWT6_A0A0V0RWT6_9BILA_6336 are exactly identical! WARNING: Sequences tr_H0YZJ0_H0YZJ0_TAEGU_59729 and tr_A0A093PU69_A0A093PU69_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZAT0_H0ZAT0_TAEGU_59729 and tr_U3K220_U3K220_FICAL_59894 are exactly identical! WARNING: Sequences tr_G1M9J5_G1M9J5_AILME_9646 and tr_A0A2U3WAQ4_A0A2U3WAQ4_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1M9J5_G1M9J5_AILME_9646 and tr_A0A2U3XPM5_A0A2U3XPM5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1M9J5_G1M9J5_AILME_9646 and tr_A0A2Y9JDN5_A0A2Y9JDN5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUW0_A0A2D0SUW0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUW8_A0A2D0SUW8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_W5KSP8_W5KSP8_ASTMX_7994 and tr_A0A2D0SUX1_A0A2D0SUX1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A087RDD6_A0A087RDD6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A091VXV9_A0A091VXV9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091UM65_A0A091UM65_NIPNI_128390 and tr_A0A0A0AMY3_A0A0A0AMY3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CQC3_A0A0V1CQC3_TRIBR_45882 and tr_A0A0V0WCH1_A0A0V0WCH1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CQC3_A0A0V1CQC3_TRIBR_45882 and tr_A0A0V1A319_A0A0V1A319_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CQC3_A0A0V1CQC3_TRIBR_45882 and tr_A0A0V1NTD5_A0A0V1NTD5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CQC3_A0A0V1CQC3_TRIBR_45882 and tr_A0A0V0UD97_A0A0V0UD97_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1D1UMV8_A0A1D1UMV8_RAMVA_947166 and tr_A0A1D1URJ9_A0A1D1URJ9_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226N2B4_A0A226N2B4_CALSU_9009 and tr_A0A226N842_A0A226N842_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N8P5_A0A226N8P5_CALSU_9009 and tr_A0A226PSY0_A0A226PSY0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PHC7_A0A2D0PHC7_ICTPU_7998 and tr_A0A2D0PIN5_A0A2D0PIN5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QQT0_A0A2D0QQT0_ICTPU_7998 and tr_A0A2D0QR01_A0A2D0QR01_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QQT0_A0A2D0QQT0_ICTPU_7998 and tr_A0A2D0QRA4_A0A2D0QRA4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBA0_A0A2D0RBA0_ICTPU_7998 and tr_W5UG84_W5UG84_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RVC0_A0A2D0RVC0_ICTPU_7998 and tr_A0A2D0RVY9_A0A2D0RVY9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3B5_A0A2D0S3B5_ICTPU_7998 and tr_A0A2D0S4V5_A0A2D0S4V5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S3B7_A0A2D0S3B7_ICTPU_7998 and tr_A0A2D0S3D4_A0A2D0S3D4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SI70_A0A2D0SI70_ICTPU_7998 and tr_W5UCZ6_W5UCZ6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SM82_A0A2D0SM82_ICTPU_7998 and tr_A0A2D0SMV3_A0A2D0SMV3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SR14_A0A2D0SR14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SR19_A0A2D0SR19_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR04_A0A2D0SR04_ICTPU_7998 and tr_A0A2D0SS55_A0A2D0SS55_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LQ80_A0A2K5LQ80_CERAT_9531 and tr_A0A2K6DPB1_A0A2K6DPB1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U4CKI3_A0A2U4CKI3_TURTR_9739 and tr_A0A2Y9LAK1_A0A2Y9LAK1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CKI3_A0A2U4CKI3_TURTR_9739 and tr_A0A383ZYH5_A0A383ZYH5_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9MW19_A0A2Y9MW19_DELLE_9749 and tr_A0A2Y9EX31_A0A2Y9EX31_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 89 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/Q96P64/3_mltree/Q96P64.raxml.reduced.phy Alignment comprises 1 partitions and 525 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 525 / 525 Gaps: 18.13 % Invariant sites: 0.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/3_mltree/Q96P64.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 263 / 21040 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -826502.352213] Initial branch length optimization [00:00:11 -674778.051624] Model parameter optimization (eps = 10.000000) [00:01:17 -672511.027410] AUTODETECT spr round 1 (radius: 5) [00:04:50 -430561.097924] AUTODETECT spr round 2 (radius: 10) [00:08:27 -301742.520253] AUTODETECT spr round 3 (radius: 15) [00:12:24 -229002.628195] AUTODETECT spr round 4 (radius: 20) [00:16:32 -216912.436180] AUTODETECT spr round 5 (radius: 25) [00:22:16 -197128.634127] SPR radius for FAST iterations: 25 (autodetect) [00:22:16 -197128.634127] Model parameter optimization (eps = 3.000000) [00:22:45 -196911.286650] FAST spr round 1 (radius: 25) [00:26:30 -163681.083380] FAST spr round 2 (radius: 25) [00:29:23 -162187.381749] FAST spr round 3 (radius: 25) [00:31:58 -162118.680973] FAST spr round 4 (radius: 25) [00:34:23 -162086.764822] FAST spr round 5 (radius: 25) [00:36:36 -162085.466684] FAST spr round 6 (radius: 25) [00:38:49 -162085.466380] Model parameter optimization (eps = 1.000000) [00:39:06 -162082.460745] SLOW spr round 1 (radius: 5) [00:42:11 -162036.281628] SLOW spr round 2 (radius: 5) [00:45:17 -162028.578753] SLOW spr round 3 (radius: 5) [00:48:14 -162028.138075] SLOW spr round 4 (radius: 5) [00:51:13 -162025.591743] SLOW spr round 5 (radius: 5) [00:54:07 -162025.591198] SLOW spr round 6 (radius: 10) [00:57:07 -162024.177819] SLOW spr round 7 (radius: 5) [01:00:42 -162024.177231] SLOW spr round 8 (radius: 10) [01:04:05 -162024.177174] SLOW spr round 9 (radius: 15) [01:08:39 -162024.177145] SLOW spr round 10 (radius: 20) [01:13:33] [worker #1] ML tree search #2, logLikelihood: -162039.749560 [01:15:24 -162024.177119] SLOW spr round 11 (radius: 25) [01:24:18 -162024.177093] Model parameter optimization (eps = 0.100000) [01:24:31] [worker #0] ML tree search #1, logLikelihood: -162023.993811 [01:24:31 -826617.701882] Initial branch length optimization [01:24:39 -673445.743469] Model parameter optimization (eps = 10.000000) [01:25:37 -671100.881301] AUTODETECT spr round 1 (radius: 5) [01:29:09 -436533.159936] AUTODETECT spr round 2 (radius: 10) [01:32:48 -293701.432920] AUTODETECT spr round 3 (radius: 15) [01:36:41 -228268.459332] AUTODETECT spr round 4 (radius: 20) [01:41:04 -199303.853770] AUTODETECT spr round 5 (radius: 25) [01:45:39 -190946.618608] SPR radius for FAST iterations: 25 (autodetect) [01:45:39 -190946.618608] Model parameter optimization (eps = 3.000000) [01:46:12 -190741.282165] FAST spr round 1 (radius: 25) [01:50:06 -163796.337720] FAST spr round 2 (radius: 25) [01:53:09 -162220.709659] FAST spr round 3 (radius: 25) [01:55:50 -162114.061151] FAST spr round 4 (radius: 25) [01:58:18 -162070.971684] FAST spr round 5 (radius: 25) [02:00:34 -162069.527822] FAST spr round 6 (radius: 25) [02:01:39] [worker #2] ML tree search #3, logLikelihood: -162048.809526 [02:02:45 -162069.527697] Model parameter optimization (eps = 1.000000) [02:03:04 -162064.973410] SLOW spr round 1 (radius: 5) [02:06:10 -162040.412574] SLOW spr round 2 (radius: 5) [02:09:10 -162039.498673] SLOW spr round 3 (radius: 5) [02:12:06 -162039.495961] SLOW spr round 4 (radius: 10) [02:15:10 -162039.272218] SLOW spr round 5 (radius: 5) [02:18:46 -162039.271886] SLOW spr round 6 (radius: 10) [02:22:09 -162039.271843] SLOW spr round 7 (radius: 15) [02:26:47 -162039.271816] SLOW spr round 8 (radius: 20) [02:29:59] [worker #1] ML tree search #5, logLikelihood: -162037.638511 [02:33:49 -162039.271789] SLOW spr round 9 (radius: 25) [02:42:53 -162039.271763] Model parameter optimization (eps = 0.100000) [02:43:03] [worker #0] ML tree search #4, logLikelihood: -162039.173723 [02:43:03 -823350.277462] Initial branch length optimization [02:43:11 -672302.754930] Model parameter optimization (eps = 10.000000) [02:43:57 -670138.526174] AUTODETECT spr round 1 (radius: 5) [02:47:28 -430069.888391] AUTODETECT spr round 2 (radius: 10) [02:51:02 -306274.412943] AUTODETECT spr round 3 (radius: 15) [02:55:10 -233745.730887] AUTODETECT spr round 4 (radius: 20) [03:00:05 -196320.467688] AUTODETECT spr round 5 (radius: 25) [03:05:51 -189760.382375] SPR radius for FAST iterations: 25 (autodetect) [03:05:51 -189760.382375] Model parameter optimization (eps = 3.000000) [03:06:25 -189562.276008] FAST spr round 1 (radius: 25) [03:10:23 -163307.468546] FAST spr round 2 (radius: 25) [03:13:27 -162299.059572] FAST spr round 3 (radius: 25) [03:15:19] [worker #2] ML tree search #6, logLikelihood: -162027.729489 [03:16:02 -162098.302444] FAST spr round 4 (radius: 25) [03:18:25 -162092.673241] FAST spr round 5 (radius: 25) [03:20:41 -162091.433068] FAST spr round 6 (radius: 25) [03:22:51 -162091.432227] Model parameter optimization (eps = 1.000000) [03:23:09 -162086.384578] SLOW spr round 1 (radius: 5) [03:26:14 -162044.378165] SLOW spr round 2 (radius: 5) [03:29:18 -162036.147679] SLOW spr round 3 (radius: 5) [03:32:14 -162036.147010] SLOW spr round 4 (radius: 10) [03:35:16 -162035.264248] SLOW spr round 5 (radius: 5) [03:38:52 -162035.263519] SLOW spr round 6 (radius: 10) [03:42:17 -162035.263451] SLOW spr round 7 (radius: 15) [03:46:58 -162035.263423] SLOW spr round 8 (radius: 20) [03:50:22] [worker #1] ML tree search #8, logLikelihood: -162031.972478 [03:54:04 -162035.263398] SLOW spr round 9 (radius: 25) [04:03:22 -162035.263372] Model parameter optimization (eps = 0.100000) [04:03:32] [worker #0] ML tree search #7, logLikelihood: -162035.088666 [04:03:32 -824763.553105] Initial branch length optimization [04:03:41 -675431.124220] Model parameter optimization (eps = 10.000000) [04:04:33 -673118.024459] AUTODETECT spr round 1 (radius: 5) [04:08:02 -423065.003591] AUTODETECT spr round 2 (radius: 10) [04:11:40 -300138.096078] AUTODETECT spr round 3 (radius: 15) [04:15:34 -247480.390390] AUTODETECT spr round 4 (radius: 20) [04:20:16 -211695.619919] AUTODETECT spr round 5 (radius: 25) [04:25:14 -195840.916322] SPR radius for FAST iterations: 25 (autodetect) [04:25:14 -195840.916322] Model parameter optimization (eps = 3.000000) [04:25:47 -195659.162096] FAST spr round 1 (radius: 25) [04:29:50 -164298.835077] FAST spr round 2 (radius: 25) [04:31:57] [worker #2] ML tree search #9, logLikelihood: -162041.488175 [04:32:56 -162190.009613] FAST spr round 3 (radius: 25) [04:35:32 -162118.966072] FAST spr round 4 (radius: 25) [04:37:58 -162113.328737] FAST spr round 5 (radius: 25) [04:40:14 -162111.270320] FAST spr round 6 (radius: 25) [04:42:29 -162111.270215] Model parameter optimization (eps = 1.000000) [04:42:50 -162097.474443] SLOW spr round 1 (radius: 5) [04:45:52 -162053.720519] SLOW spr round 2 (radius: 5) [04:48:57 -162041.044797] SLOW spr round 3 (radius: 5) [04:52:00 -162041.044693] SLOW spr round 4 (radius: 10) [04:55:04 -162034.832201] SLOW spr round 5 (radius: 5) [04:58:47 -162033.519399] SLOW spr round 6 (radius: 5) [05:02:04 -162033.519229] SLOW spr round 7 (radius: 10) [05:05:14] [worker #1] ML tree search #11, logLikelihood: -162039.939233 [05:05:15 -162031.385800] SLOW spr round 8 (radius: 5) [05:08:51 -162031.385653] SLOW spr round 9 (radius: 10) [05:12:13 -162031.385625] SLOW spr round 10 (radius: 15) [05:16:56 -162031.385597] SLOW spr round 11 (radius: 20) [05:24:04 -162031.385568] SLOW spr round 12 (radius: 25) [05:33:13 -162031.385540] Model parameter optimization (eps = 0.100000) [05:33:32] [worker #0] ML tree search #10, logLikelihood: -162030.989831 [05:33:32 -825793.633055] Initial branch length optimization [05:33:40 -671752.803473] Model parameter optimization (eps = 10.000000) [05:34:48 -669686.964027] AUTODETECT spr round 1 (radius: 5) [05:38:20 -426869.886433] AUTODETECT spr round 2 (radius: 10) [05:41:55 -286081.936031] AUTODETECT spr round 3 (radius: 15) [05:45:41 -245931.555728] AUTODETECT spr round 4 (radius: 20) [05:49:09] [worker #2] ML tree search #12, logLikelihood: -162044.004185 [05:50:06 -208399.266275] AUTODETECT spr round 5 (radius: 25) [05:55:51 -198024.986623] SPR radius for FAST iterations: 25 (autodetect) [05:55:51 -198024.986623] Model parameter optimization (eps = 3.000000) [05:56:27 -197829.647412] FAST spr round 1 (radius: 25) [06:00:34 -163588.035068] FAST spr round 2 (radius: 25) [06:03:42 -162179.104865] FAST spr round 3 (radius: 25) [06:06:23 -162103.888031] FAST spr round 4 (radius: 25) [06:08:47 -162096.432407] FAST spr round 5 (radius: 25) [06:11:03 -162095.784913] FAST spr round 6 (radius: 25) [06:13:16 -162095.784866] Model parameter optimization (eps = 1.000000) [06:13:35 -162089.023899] SLOW spr round 1 (radius: 5) [06:16:46 -162049.020606] SLOW spr round 2 (radius: 5) [06:19:49 -162046.714129] SLOW spr round 3 (radius: 5) [06:22:48 -162045.164714] SLOW spr round 4 (radius: 5) [06:25:16] [worker #1] ML tree search #14, logLikelihood: -162034.774471 [06:25:45 -162045.164685] SLOW spr round 5 (radius: 10) [06:28:49 -162043.611011] SLOW spr round 6 (radius: 5) [06:32:26 -162043.610930] SLOW spr round 7 (radius: 10) [06:35:48 -162043.610902] SLOW spr round 8 (radius: 15) [06:40:22 -162043.610875] SLOW spr round 9 (radius: 20) [06:47:03 -162043.610848] SLOW spr round 10 (radius: 25) [06:55:16 -162043.610821] Model parameter optimization (eps = 0.100000) [06:55:28] [worker #0] ML tree search #13, logLikelihood: -162043.149812 [06:55:28 -821795.159529] Initial branch length optimization [06:55:35 -674031.188468] Model parameter optimization (eps = 10.000000) [06:56:33 -671750.523012] AUTODETECT spr round 1 (radius: 5) [07:00:03 -427217.770787] AUTODETECT spr round 2 (radius: 10) [07:03:38 -298048.116823] AUTODETECT spr round 3 (radius: 15) [07:07:21 -236323.432200] AUTODETECT spr round 4 (radius: 20) [07:12:12 -196830.480959] AUTODETECT spr round 5 (radius: 25) [07:13:46] [worker #2] ML tree search #15, logLikelihood: -162039.356130 [07:16:55 -190325.064217] SPR radius for FAST iterations: 25 (autodetect) [07:16:55 -190325.064217] Model parameter optimization (eps = 3.000000) [07:17:27 -190157.436741] FAST spr round 1 (radius: 25) [07:21:22 -164310.184631] FAST spr round 2 (radius: 25) [07:24:21 -162165.981399] FAST spr round 3 (radius: 25) [07:26:56 -162082.631561] FAST spr round 4 (radius: 25) [07:29:21 -162073.479946] FAST spr round 5 (radius: 25) [07:31:38 -162073.479260] Model parameter optimization (eps = 1.000000) [07:31:55 -162069.940475] SLOW spr round 1 (radius: 5) [07:35:01 -162037.788879] SLOW spr round 2 (radius: 5) [07:38:06 -162037.376875] SLOW spr round 3 (radius: 5) [07:41:00] [worker #1] ML tree search #17, logLikelihood: -162027.989823 [07:41:02 -162037.374812] SLOW spr round 4 (radius: 10) [07:44:06 -162035.091207] SLOW spr round 5 (radius: 5) [07:47:43 -162035.090931] SLOW spr round 6 (radius: 10) [07:51:06 -162035.090896] SLOW spr round 7 (radius: 15) [07:55:43 -162035.090870] SLOW spr round 8 (radius: 20) [08:02:44 -162035.090845] SLOW spr round 9 (radius: 25) [08:11:48 -162035.090820] Model parameter optimization (eps = 0.100000) [08:12:02] [worker #0] ML tree search #16, logLikelihood: -162034.839854 [08:12:02 -811830.365597] Initial branch length optimization [08:12:10 -665787.442176] Model parameter optimization (eps = 10.000000) [08:13:17 -663746.964932] AUTODETECT spr round 1 (radius: 5) [08:16:51 -422023.135786] AUTODETECT spr round 2 (radius: 10) [08:20:30 -282768.605873] AUTODETECT spr round 3 (radius: 15) [08:24:32 -214102.949535] AUTODETECT spr round 4 (radius: 20) [08:29:12 -196216.565123] AUTODETECT spr round 5 (radius: 25) [08:34:24 -193402.002447] SPR radius for FAST iterations: 25 (autodetect) [08:34:24 -193402.002447] Model parameter optimization (eps = 3.000000) [08:35:03 -193208.903565] FAST spr round 1 (radius: 25) [08:38:43 -162959.179478] FAST spr round 2 (radius: 25) [08:41:38 -162113.286559] FAST spr round 3 (radius: 25) [08:44:12 -162095.397507] FAST spr round 4 (radius: 25) [08:46:32 -162094.425531] FAST spr round 5 (radius: 25) [08:48:45 -162094.424110] Model parameter optimization (eps = 1.000000) [08:49:08 -162085.936459] SLOW spr round 1 (radius: 5) [08:51:33] [worker #2] ML tree search #18, logLikelihood: -162050.018732 [08:52:12 -162053.966464] SLOW spr round 2 (radius: 5) [08:55:14] [worker #1] ML tree search #20, logLikelihood: -162032.590503 [08:55:17 -162048.572191] SLOW spr round 3 (radius: 5) [08:58:15 -162048.164488] SLOW spr round 4 (radius: 5) [09:01:08 -162048.164455] SLOW spr round 5 (radius: 10) [09:04:09 -162046.231300] SLOW spr round 6 (radius: 5) [09:07:47 -162045.904446] SLOW spr round 7 (radius: 5) [09:11:02 -162045.904400] SLOW spr round 8 (radius: 10) [09:14:12 -162045.904371] SLOW spr round 9 (radius: 15) [09:18:59 -162045.474465] SLOW spr round 10 (radius: 5) [09:22:47 -162044.057259] SLOW spr round 11 (radius: 5) [09:26:08 -162044.057160] SLOW spr round 12 (radius: 10) [09:29:22 -162044.057127] SLOW spr round 13 (radius: 15) [09:34:07 -162044.057098] SLOW spr round 14 (radius: 20) [09:41:35 -162044.057069] SLOW spr round 15 (radius: 25) [09:51:11 -162044.057041] Model parameter optimization (eps = 0.100000) [09:51:22] [worker #0] ML tree search #19, logLikelihood: -162043.937096 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.147082,0.353791) (0.120822,0.530924) (0.457454,0.887371) (0.274641,1.740032) 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: -162023.993811 AIC score: 328057.987623 / AICc score: 8372117.987623 / BIC score: 336606.101139 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=525). 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/Q96P64/3_mltree/Q96P64.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/3_mltree/Q96P64.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/3_mltree/Q96P64.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P64/3_mltree/Q96P64.raxml.log Analysis started: 01-Jul-2021 20:25:00 / finished: 02-Jul-2021 06:16:22 Elapsed time: 35482.356 seconds Consumed energy: 3098.102 Wh (= 15 km in an electric car, or 77 km with an e-scooter!)