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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 04-Jun-2021 17:15:12 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/2_msa/P04264_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264 --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/020621_run/phylogeny-snakemake/results/P04264/2_msa/P04264_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 335 sites WARNING: Sequences tr_A0A1D5PXP0_A0A1D5PXP0_CHICK_9031 and tr_G1NER8_G1NER8_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q9DCV7_K2C7_MOUSE_10090 and sp_Q6IG12_K2C7_RAT_10116 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_G3QKU2_G3QKU2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_H2NHD7_H2NHD7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and sp_A5A6M8_K2C5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_H2Q5Z8_H2Q5Z8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and sp_P13647_K2C5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and tr_H2Q5Z9_H2Q5Z9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and sp_Q3SY84_K2C71_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and tr_A0A2R9B4E9_A0A2R9B4E9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKU7_G3QKU7_GORGO_9595 and tr_H2RGY7_H2RGY7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKU7_G3QKU7_GORGO_9595 and tr_A0A2R9AZS5_A0A2R9AZS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QLP7_G3QLP7_GORGO_9595 and tr_H2R1Z0_H2R1Z0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QLP7_G3QLP7_GORGO_9595 and sp_P04264_K2C1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2J8KDC3_A0A2J8KDC3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and sp_P05787_K2C8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2R9A6T6_A0A2R9A6T6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NHE7_H2NHE7_PONAB_9601 and tr_H2Q605_H2Q605_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1SY72_G1SY72_RABIT_9986 and sp_Q29426_K2C3_RABIT_9986 are exactly identical! WARNING: Sequences tr_F1PTY1_F1PTY1_CANLF_9615 and sp_Q6EIY9_K2C1_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3TV17_A0A2I3TV17_PANTR_9598 and sp_P12035_K2C3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TV17_A0A2I3TV17_PANTR_9598 and tr_A0A2R9A6B3_A0A2R9A6B3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KDF1_A0A2J8KDF1_PANTR_9598 and tr_A0A2R9CPA3_A0A2R9CPA3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q602_H2Q602_PANTR_9598 and tr_A0A2R9ANL2_A0A2R9ANL2_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q671_W5Q671_SHEEP_9940 and sp_Q148H5_K2C71_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P02538_K2C6A_HUMAN_9606 and tr_A0A2R9B125_A0A2R9B125_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QW39_A0A1D5QW39_MACMU_9544 and tr_A0A2K6BIH7_A0A2K6BIH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RKK9_A0A1D5RKK9_MACMU_9544 and tr_A0A2K6DEK3_A0A2K6DEK3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A096MVH8_A0A096MVH8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A2K6DMD1_A0A2K6DMD1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A2K5ZK75_A0A2K5ZK75_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7AEN7_F7AEN7_MACMU_9544 and tr_A0A2K6BPE2_A0A2K6BPE2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A096NAU0_A0A096NAU0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A0D9R013_A0A0D9R013_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A2K5MDQ1_A0A2K5MDQ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A2K6CZV9_A0A2K6CZV9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A2K5XIW4_A0A2K5XIW4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_G7PIC5_G7PIC5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A096ML93_A0A096ML93_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K5KH39_A0A2K5KH39_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K6B509_A0A2K6B509_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K6AJ14_A0A2K6AJ14_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HGY2_F7HGY2_MACMU_9544 and tr_A0A2K6CR37_A0A2K6CR37_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A096MSQ9_A0A096MSQ9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K5N2V1_A0A2K5N2V1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K6BED4_A0A2K6BED4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PID4_G7PID4_MACFA_9541 and tr_A0A0D9QZZ8_A0A0D9QZZ8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PID4_G7PID4_MACFA_9541 and tr_A0A2K6C019_A0A2K6C019_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PID4_G7PID4_MACFA_9541 and tr_A0A2K5YE01_A0A2K5YE01_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PID6_G7PID6_MACFA_9541 and tr_A0A096N9P6_A0A096N9P6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A5D7M6_A5D7M6_BOVIN_9913 and sp_Q5XQN5_K2C5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MPX0_A0A096MPX0_PAPAN_9555 and tr_A0A2K5LH62_A0A2K5LH62_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4V8_A0A096N4V8_PAPAN_9555 and tr_A0A2K5N3I3_A0A2K5N3I3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4V8_A0A096N4V8_PAPAN_9555 and tr_A0A2K6A0H6_A0A2K6A0H6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N512_A0A096N512_PAPAN_9555 and tr_A0A0D9R016_A0A0D9R016_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096N512_A0A096N512_PAPAN_9555 and tr_A0A2K5P1T1_A0A2K5P1T1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N512_A0A096N512_PAPAN_9555 and tr_A0A2K5XUJ7_A0A2K5XUJ7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K5NJ30_A0A2K5NJ30_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K6E7G3_A0A2K6E7G3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 and tr_A0A2K5XF23_A0A2K5XF23_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QZY9_A0A0D9QZY9_CHLSB_60711 and tr_A0A2K5ZTU8_A0A2K5ZTU8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A226MN28_A0A226MN28_CALSU_9009 and tr_A0A226NV08_A0A226NV08_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MNG6_A0A226MNG6_CALSU_9009 and tr_A0A226PU49_A0A226PU49_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5MWZ1_A0A2K5MWZ1_CERAT_9531 and tr_A0A2K6AJW7_A0A2K6AJW7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3WCU6_A0A2U3WCU6_ODORO_9708 and tr_A0A2U3YQ66_A0A2U3YQ66_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3YQ72_A0A2U3YQ72_LEPWE_9713 and tr_A0A2Y9KMG2_A0A2Y9KMG2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3YQ72_A0A2U3YQ72_LEPWE_9713 and tr_A0A384D7D7_A0A384D7D7_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 67 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.reduced.phy Alignment comprises 1 partitions and 335 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 335 / 335 Gaps: 0.22 % Invariant sites: 1.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 335 / 26800 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -313127.768003] Initial branch length optimization [00:00:09 -278395.880261] Model parameter optimization (eps = 10.000000) [00:01:01 -276134.512882] AUTODETECT spr round 1 (radius: 5) [00:04:57 -197844.409487] AUTODETECT spr round 2 (radius: 10) [00:08:57 -137726.141976] AUTODETECT spr round 3 (radius: 15) [00:13:42 -117542.238870] AUTODETECT spr round 4 (radius: 20) [00:20:18 -103661.121218] AUTODETECT spr round 5 (radius: 25) [00:29:19 -102883.611185] SPR radius for FAST iterations: 25 (autodetect) [00:29:19 -102883.611185] Model parameter optimization (eps = 3.000000) [00:29:58 -102846.429443] FAST spr round 1 (radius: 25) [00:34:04 -88529.467638] FAST spr round 2 (radius: 25) [00:37:01 -87432.080050] FAST spr round 3 (radius: 25) [00:39:43 -87398.888102] FAST spr round 4 (radius: 25) [00:42:03 -87393.132357] FAST spr round 5 (radius: 25) [00:44:15 -87393.132355] Model parameter optimization (eps = 1.000000) [00:44:36 -87387.914887] SLOW spr round 1 (radius: 5) [00:48:07 -87366.101366] SLOW spr round 2 (radius: 5) [00:51:21 -87364.367853] SLOW spr round 3 (radius: 5) [00:54:26 -87364.367828] SLOW spr round 4 (radius: 10) [00:57:34 -87352.181927] SLOW spr round 5 (radius: 5) [01:01:44 -87352.181611] SLOW spr round 6 (radius: 10) [01:05:11 -87352.181609] SLOW spr round 7 (radius: 15) [01:10:37 -87352.181609] SLOW spr round 8 (radius: 20) [01:21:51 -87352.181609] SLOW spr round 9 (radius: 25) [01:35:17] [worker #2] ML tree search #3, logLikelihood: -87337.022531 [01:36:24] [worker #4] ML tree search #5, logLikelihood: -87341.104554 [01:36:47 -87352.181609] Model parameter optimization (eps = 0.100000) [01:36:54] [worker #0] ML tree search #1, logLikelihood: -87352.171923 [01:36:54 -314257.655837] Initial branch length optimization [01:37:02 -278134.977700] Model parameter optimization (eps = 10.000000) [01:37:54 -275896.094532] AUTODETECT spr round 1 (radius: 5) [01:41:52 -196307.400558] AUTODETECT spr round 2 (radius: 10) [01:45:48 -126604.652335] AUTODETECT spr round 3 (radius: 15) [01:47:25] [worker #3] ML tree search #4, logLikelihood: -87351.155037 [01:49:28] [worker #1] ML tree search #2, logLikelihood: -87356.897363 [01:50:22 -105950.661810] AUTODETECT spr round 4 (radius: 20) [01:56:30 -101428.042790] AUTODETECT spr round 5 (radius: 25) [02:03:30 -99606.789692] SPR radius for FAST iterations: 25 (autodetect) [02:03:30 -99606.789692] Model parameter optimization (eps = 3.000000) [02:03:59 -99585.029634] FAST spr round 1 (radius: 25) [02:07:57 -88020.261984] FAST spr round 2 (radius: 25) [02:10:50 -87509.200591] FAST spr round 3 (radius: 25) [02:13:24 -87429.261051] FAST spr round 4 (radius: 25) [02:15:42 -87426.147901] FAST spr round 5 (radius: 25) [02:17:53 -87426.146211] Model parameter optimization (eps = 1.000000) [02:18:11 -87419.717156] SLOW spr round 1 (radius: 5) [02:21:41 -87376.973478] SLOW spr round 2 (radius: 5) [02:25:03 -87370.758112] SLOW spr round 3 (radius: 5) [02:28:17 -87355.268319] SLOW spr round 4 (radius: 5) [02:31:24 -87353.833484] SLOW spr round 5 (radius: 5) [02:34:25 -87352.417668] SLOW spr round 6 (radius: 5) [02:37:24 -87352.417652] SLOW spr round 7 (radius: 10) [02:40:37 -87349.408231] SLOW spr round 8 (radius: 5) [02:45:03 -87331.844793] SLOW spr round 9 (radius: 5) [02:48:43 -87331.689395] SLOW spr round 10 (radius: 5) [02:52:02 -87331.689207] SLOW spr round 11 (radius: 10) [02:55:14 -87330.647119] SLOW spr round 12 (radius: 5) [02:59:26 -87330.624474] SLOW spr round 13 (radius: 10) [03:02:56 -87330.550763] SLOW spr round 14 (radius: 15) [03:08:19 -87330.550169] SLOW spr round 15 (radius: 20) [03:19:34 -87330.549899] SLOW spr round 16 (radius: 25) [03:28:41] [worker #2] ML tree search #8, logLikelihood: -87321.505342 [03:33:56 -87330.549785] Model parameter optimization (eps = 0.100000) [03:34:11] [worker #0] ML tree search #6, logLikelihood: -87329.647415 [03:34:12 -315606.751933] Initial branch length optimization [03:34:21 -279038.665048] Model parameter optimization (eps = 10.000000) [03:35:13 -276761.171601] AUTODETECT spr round 1 (radius: 5) [03:39:09 -200225.629197] AUTODETECT spr round 2 (radius: 10) [03:40:04] [worker #3] ML tree search #9, logLikelihood: -87342.547342 [03:41:14] [worker #1] ML tree search #7, logLikelihood: -87339.348637 [03:43:01 -130888.506284] AUTODETECT spr round 3 (radius: 15) [03:47:20 -109986.395638] AUTODETECT spr round 4 (radius: 20) [03:53:09 -101123.707825] AUTODETECT spr round 5 (radius: 25) [03:55:07] [worker #4] ML tree search #10, logLikelihood: -87361.534530 [04:01:06 -100565.001405] SPR radius for FAST iterations: 25 (autodetect) [04:01:06 -100565.001405] Model parameter optimization (eps = 3.000000) [04:01:34 -100539.246192] FAST spr round 1 (radius: 25) [04:05:27 -87905.302185] FAST spr round 2 (radius: 25) [04:08:25 -87429.386726] FAST spr round 3 (radius: 25) [04:11:04 -87381.933806] FAST spr round 4 (radius: 25) [04:13:20 -87381.009973] FAST spr round 5 (radius: 25) [04:15:31 -87381.009946] Model parameter optimization (eps = 1.000000) [04:15:49 -87377.032237] SLOW spr round 1 (radius: 5) [04:19:19 -87345.251373] SLOW spr round 2 (radius: 5) [04:22:30 -87342.653852] SLOW spr round 3 (radius: 5) [04:25:33 -87342.653846] SLOW spr round 4 (radius: 10) [04:28:38 -87340.382589] SLOW spr round 5 (radius: 5) [04:32:55 -87336.833843] SLOW spr round 6 (radius: 5) [04:36:40 -87336.329086] SLOW spr round 7 (radius: 5) [04:40:04 -87335.103707] SLOW spr round 8 (radius: 5) [04:43:12 -87335.103690] SLOW spr round 9 (radius: 10) [04:46:15 -87335.052094] SLOW spr round 10 (radius: 15) [04:51:55 -87335.052094] SLOW spr round 11 (radius: 20) [05:02:56 -87335.052094] SLOW spr round 12 (radius: 25) [05:10:33] [worker #1] ML tree search #12, logLikelihood: -87357.480371 [05:18:03 -87335.052094] Model parameter optimization (eps = 0.100000) [05:18:17] [worker #0] ML tree search #11, logLikelihood: -87333.951438 [05:18:17 -314059.718883] Initial branch length optimization [05:18:26 -277819.121098] Model parameter optimization (eps = 10.000000) [05:19:25 -275591.117610] AUTODETECT spr round 1 (radius: 5) [05:23:22 -197111.221312] AUTODETECT spr round 2 (radius: 10) [05:27:19 -132062.652331] AUTODETECT spr round 3 (radius: 15) [05:31:50 -103696.147141] AUTODETECT spr round 4 (radius: 20) [05:34:44] [worker #3] ML tree search #14, logLikelihood: -87364.458557 [05:37:53 -100407.422297] AUTODETECT spr round 5 (radius: 25) [05:41:53] [worker #2] ML tree search #13, logLikelihood: -87339.968673 [05:43:29] [worker #4] ML tree search #15, logLikelihood: -87348.244417 [05:46:21 -99549.818573] SPR radius for FAST iterations: 25 (autodetect) [05:46:21 -99549.818573] Model parameter optimization (eps = 3.000000) [05:46:53 -99506.865885] FAST spr round 1 (radius: 25) [05:50:48 -87957.677606] FAST spr round 2 (radius: 25) [05:53:43 -87491.896952] FAST spr round 3 (radius: 25) [05:56:19 -87420.798624] FAST spr round 4 (radius: 25) [05:58:45 -87393.056686] FAST spr round 5 (radius: 25) [06:00:56 -87391.754640] FAST spr round 6 (radius: 25) [06:03:05 -87391.754637] Model parameter optimization (eps = 1.000000) [06:03:28 -87385.741650] SLOW spr round 1 (radius: 5) [06:06:52 -87353.225387] SLOW spr round 2 (radius: 5) [06:10:09 -87348.849164] SLOW spr round 3 (radius: 5) [06:13:13 -87347.104026] SLOW spr round 4 (radius: 5) [06:16:13 -87347.103995] SLOW spr round 5 (radius: 10) [06:19:22 -87345.709119] SLOW spr round 6 (radius: 5) [06:23:44 -87337.342640] SLOW spr round 7 (radius: 5) [06:27:25 -87337.342621] SLOW spr round 8 (radius: 10) [06:30:39 -87336.999717] SLOW spr round 9 (radius: 5) [06:34:50 -87336.999628] SLOW spr round 10 (radius: 10) [06:38:19 -87336.775772] SLOW spr round 11 (radius: 5) [06:42:30 -87333.863464] SLOW spr round 12 (radius: 5) [06:46:05 -87333.559627] SLOW spr round 13 (radius: 5) [06:49:24 -87330.873028] SLOW spr round 14 (radius: 5) [06:52:30 -87330.873009] SLOW spr round 15 (radius: 10) [06:55:41 -87330.400818] SLOW spr round 16 (radius: 5) [06:59:53 -87329.715134] SLOW spr round 17 (radius: 5) [07:03:32 -87328.561496] SLOW spr round 18 (radius: 5) [07:06:48 -87328.561492] SLOW spr round 19 (radius: 10) [07:08:50] [worker #1] ML tree search #17, logLikelihood: -87356.698389 [07:09:57 -87328.561492] SLOW spr round 20 (radius: 15) [07:15:42 -87328.561492] SLOW spr round 21 (radius: 20) [07:18:16] [worker #3] ML tree search #19, logLikelihood: -87357.978647 [07:26:46 -87328.561492] SLOW spr round 22 (radius: 25) [07:28:00] [worker #4] ML tree search #20, logLikelihood: -87347.775081 [07:42:47 -87328.561492] Model parameter optimization (eps = 0.100000) [07:42:55] [worker #0] ML tree search #16, logLikelihood: -87328.482973 [07:58:04] [worker #2] ML tree search #18, logLikelihood: -87350.249945 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.352681,0.466885) (0.272015,0.687742) (0.301597,1.474136) (0.073707,2.763195) 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: -87321.505342 AIC score: 178653.010684 / AICc score: 8222713.010684 / BIC score: 186300.342400 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=335). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 136 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04264/3_mltree/P04264.raxml.log Analysis started: 04-Jun-2021 17:15:12 / finished: 05-Jun-2021 01:13:17 Elapsed time: 28684.410 seconds Consumed energy: 2443.354 Wh (= 12 km in an electric car, or 61 km with an e-scooter!)