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 03-Jul-2021 07:53:39 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/2_msa/P01763_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/3_mltree/P01763 --seed 2 --threads 3 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/2_msa/P01763_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 138 sites WARNING: Sequences sp_P01787_HVM18_MOUSE_10090 and sp_P01788_HVM19_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01796_HVM27_MOUSE_10090 and sp_P01797_HVM28_MOUSE_10090 are exactly identical! WARNING: Sequences tr_G1PB40_G1PB40_MYOLU_59463 and tr_G1Q1K2_G1Q1K2_MYOLU_59463 are exactly identical! WARNING: Sequences tr_A0A2I3SLP9_A0A2I3SLP9_PANTR_9598 and tr_A0A2R8ZD36_A0A2R8ZD36_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TKW9_A0A2I3TKW9_PANTR_9598 and tr_A0A2R8Z8X7_A0A2R8Z8X7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UMB9_F6UMB9_ORNAN_9258 and tr_F6WX17_F6WX17_ORNAN_9258 are exactly identical! WARNING: Sequences tr_A0A0G2JT95_A0A0G2JT95_RAT_10116 and tr_M0R8Q9_M0R8Q9_RAT_10116 are exactly identical! WARNING: Sequences sp_P01768_HV330_HUMAN_9606 and sp_P0DP03_HV335_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G8F4H5_G8F4H5_MACFA_9541 and tr_A0A0D9R9X1_A0A0D9R9X1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3M2H8_A0A2I3M2H8_PAPAN_9555 and tr_A0A2K5XS06_A0A2K5XS06_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 10 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/P01763/3_mltree/P01763.raxml.reduced.phy Alignment comprises 1 partitions and 138 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 138 / 138 Gaps: 17.03 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/3_mltree/P01763.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -135409.921656] Initial branch length optimization [00:00:02 -118274.155001] Model parameter optimization (eps = 10.000000) [00:00:36 -117650.603731] AUTODETECT spr round 1 (radius: 5) [00:02:52 -104248.155702] AUTODETECT spr round 2 (radius: 10) [00:05:42 -87032.606438] AUTODETECT spr round 3 (radius: 15) [00:08:54 -74937.141435] AUTODETECT spr round 4 (radius: 20) [00:12:16 -69900.393563] AUTODETECT spr round 5 (radius: 25) [00:16:34 -68843.472425] SPR radius for FAST iterations: 25 (autodetect) [00:16:34 -68843.472425] Model parameter optimization (eps = 3.000000) [00:16:50 -68782.006910] FAST spr round 1 (radius: 25) [00:20:47 -61576.423413] FAST spr round 2 (radius: 25) [00:23:46 -61075.401802] FAST spr round 3 (radius: 25) [00:26:05 -61023.008025] FAST spr round 4 (radius: 25) [00:28:09 -61014.345731] FAST spr round 5 (radius: 25) [00:30:03 -61012.742019] FAST spr round 6 (radius: 25) [00:31:51 -61012.741911] Model parameter optimization (eps = 1.000000) [00:32:08 -61006.328012] SLOW spr round 1 (radius: 5) [00:34:25 -60979.280376] SLOW spr round 2 (radius: 5) [00:36:49 -60974.486014] SLOW spr round 3 (radius: 5) [00:39:13 -60972.594445] SLOW spr round 4 (radius: 5) [00:41:35 -60970.798044] SLOW spr round 5 (radius: 5) [00:43:46 -60970.798026] SLOW spr round 6 (radius: 10) [00:46:03 -60968.815251] SLOW spr round 7 (radius: 5) [00:48:40 -60968.814601] SLOW spr round 8 (radius: 10) [00:50:51 -60968.814510] SLOW spr round 9 (radius: 15) [00:54:40 -60968.702259] SLOW spr round 10 (radius: 5) [00:57:45 -60967.423952] SLOW spr round 11 (radius: 5) [01:00:12 -60967.423948] SLOW spr round 12 (radius: 10) [01:02:33 -60967.423948] SLOW spr round 13 (radius: 15) [01:06:22 -60967.423948] SLOW spr round 14 (radius: 20) [01:12:09 -60967.423948] SLOW spr round 15 (radius: 25) [01:20:57 -60967.423948] Model parameter optimization (eps = 0.100000) [01:21:13] [worker #0] ML tree search #1, logLikelihood: -60967.265841 [01:21:13 -135510.043329] Initial branch length optimization [01:21:15 -118091.154259] Model parameter optimization (eps = 10.000000) [01:21:47 -117496.444426] AUTODETECT spr round 1 (radius: 5) [01:23:58 -105076.989398] AUTODETECT spr round 2 (radius: 10) [01:26:50 -87163.149331] AUTODETECT spr round 3 (radius: 15) [01:30:04 -73795.819884] AUTODETECT spr round 4 (radius: 20) [01:34:00 -69480.567449] AUTODETECT spr round 5 (radius: 25) [01:40:18 -68545.354040] SPR radius for FAST iterations: 25 (autodetect) [01:40:18 -68545.354040] Model parameter optimization (eps = 3.000000) [01:40:39 -68480.586422] FAST spr round 1 (radius: 25) [01:45:28 -61652.222128] FAST spr round 2 (radius: 25) [01:48:32 -61094.380496] FAST spr round 3 (radius: 25) [01:51:02 -61048.089919] FAST spr round 4 (radius: 25) [01:53:12 -61044.433736] FAST spr round 5 (radius: 25) [01:55:13 -61044.355145] Model parameter optimization (eps = 1.000000) [01:55:20 -61044.262627] SLOW spr round 1 (radius: 5) [01:58:01 -61023.320166] SLOW spr round 2 (radius: 5) [02:00:32 -61020.694008] SLOW spr round 3 (radius: 5) [02:02:58 -61017.573081] SLOW spr round 4 (radius: 5) [02:04:32] [worker #2] ML tree search #3, logLikelihood: -60961.932269 [02:05:22 -61015.615024] SLOW spr round 5 (radius: 5) [02:07:43 -61015.614882] SLOW spr round 6 (radius: 10) [02:10:11 -61011.012232] SLOW spr round 7 (radius: 5) [02:13:09 -61003.961395] SLOW spr round 8 (radius: 5) [02:15:48 -61003.959277] SLOW spr round 9 (radius: 10) [02:18:27 -61002.556136] SLOW spr round 10 (radius: 5) [02:21:22 -61002.541441] SLOW spr round 11 (radius: 10) [02:24:03 -61001.872871] SLOW spr round 12 (radius: 5) [02:26:54 -61001.872815] SLOW spr round 13 (radius: 10) [02:29:34 -61001.726221] SLOW spr round 14 (radius: 5) [02:32:29 -61001.207047] SLOW spr round 15 (radius: 5) [02:35:05 -61001.206571] SLOW spr round 16 (radius: 10) [02:37:38 -61001.192067] SLOW spr round 17 (radius: 15) [02:42:28 -60996.753648] SLOW spr round 18 (radius: 5) [02:45:33 -60993.675009] SLOW spr round 19 (radius: 5) [02:48:14 -60993.674961] SLOW spr round 20 (radius: 10) [02:50:48 -60993.044158] SLOW spr round 21 (radius: 5) [02:53:45 -60989.751659] SLOW spr round 22 (radius: 5) [02:56:28 -60987.432783] SLOW spr round 23 (radius: 5) [02:58:56 -60987.431656] SLOW spr round 24 (radius: 10) [03:01:23 -60987.431554] SLOW spr round 25 (radius: 15) [03:06:11 -60987.431544] SLOW spr round 26 (radius: 20) [03:14:04 -60987.431543] SLOW spr round 27 (radius: 25) [03:18:19] [worker #1] ML tree search #2, logLikelihood: -60993.368745 [03:24:15 -60987.431543] Model parameter optimization (eps = 0.100000) [03:24:28] [worker #0] ML tree search #4, logLikelihood: -60986.354773 [03:24:28 -135329.237313] Initial branch length optimization [03:24:30 -118157.913335] Model parameter optimization (eps = 10.000000) [03:25:05 -117674.924225] AUTODETECT spr round 1 (radius: 5) [03:27:29 -105162.415506] AUTODETECT spr round 2 (radius: 10) [03:30:32 -88018.259839] AUTODETECT spr round 3 (radius: 15) [03:34:07 -76136.391665] AUTODETECT spr round 4 (radius: 20) [03:38:22 -71088.297897] AUTODETECT spr round 5 (radius: 25) [03:44:23 -69305.278884] SPR radius for FAST iterations: 25 (autodetect) [03:44:23 -69305.278884] Model parameter optimization (eps = 3.000000) [03:44:46 -69236.556962] FAST spr round 1 (radius: 25) [03:49:21 -62159.652022] FAST spr round 2 (radius: 25) [03:52:17 -61308.470562] FAST spr round 3 (radius: 25) [03:54:46 -61119.915590] FAST spr round 4 (radius: 25) [03:57:05 -61088.744166] FAST spr round 5 (radius: 25) [03:59:12 -61078.135010] FAST spr round 6 (radius: 25) [04:01:09 -61076.295199] FAST spr round 7 (radius: 25) [04:03:06 -61076.294890] Model parameter optimization (eps = 1.000000) [04:03:22 -61071.928984] SLOW spr round 1 (radius: 5) [04:05:57 -61041.150638] SLOW spr round 2 (radius: 5) [04:08:23 -61040.491922] SLOW spr round 3 (radius: 5) [04:10:46 -61040.491773] SLOW spr round 4 (radius: 10) [04:13:14 -61038.851979] SLOW spr round 5 (radius: 5) [04:16:11 -61038.851975] SLOW spr round 6 (radius: 10) [04:18:57 -61037.049456] SLOW spr round 7 (radius: 5) [04:21:53 -61037.049287] SLOW spr round 8 (radius: 10) [04:24:34 -61037.049287] SLOW spr round 9 (radius: 15) [04:29:26 -61019.927753] SLOW spr round 10 (radius: 5) [04:32:33 -61018.764311] SLOW spr round 11 (radius: 5) [04:35:18 -61018.764295] SLOW spr round 12 (radius: 10) [04:37:54 -61017.174934] SLOW spr round 13 (radius: 5) [04:40:49 -61017.174783] SLOW spr round 14 (radius: 10) [04:43:32 -61017.174783] SLOW spr round 15 (radius: 15) [04:48:15 -61017.174783] SLOW spr round 16 (radius: 20) [04:50:53] [worker #2] ML tree search #6, logLikelihood: -60983.065600 [04:56:37 -61017.174783] SLOW spr round 17 (radius: 25) [05:05:54 -61013.907577] SLOW spr round 18 (radius: 5) [05:09:02 -61013.907559] SLOW spr round 19 (radius: 10) [05:12:02 -61009.103545] SLOW spr round 20 (radius: 5) [05:15:00 -60992.251542] SLOW spr round 21 (radius: 5) [05:17:39 -60991.940926] SLOW spr round 22 (radius: 5) [05:20:07 -60991.940887] SLOW spr round 23 (radius: 10) [05:22:37 -60989.068363] SLOW spr round 24 (radius: 5) [05:25:34 -60989.068303] SLOW spr round 25 (radius: 10) [05:28:18 -60989.068303] SLOW spr round 26 (radius: 15) [05:33:00 -60988.845455] SLOW spr round 27 (radius: 5) [05:36:07 -60988.102000] SLOW spr round 28 (radius: 5) [05:38:52 -60988.101747] SLOW spr round 29 (radius: 10) [05:41:28 -60988.101747] SLOW spr round 30 (radius: 15) [05:46:21 -60988.101747] SLOW spr round 31 (radius: 20) [05:54:36 -60986.135387] SLOW spr round 32 (radius: 5) [05:57:43 -60984.011465] SLOW spr round 33 (radius: 5) [06:00:29 -60984.011465] SLOW spr round 34 (radius: 10) [06:03:05 -60984.011465] SLOW spr round 35 (radius: 15) [06:08:00 -60983.996333] SLOW spr round 36 (radius: 20) [06:16:25 -60983.192276] SLOW spr round 37 (radius: 5) [06:19:34 -60974.991639] SLOW spr round 38 (radius: 5) [06:22:20 -60974.991637] SLOW spr round 39 (radius: 10) [06:24:57 -60974.991637] SLOW spr round 40 (radius: 15) [06:29:52 -60974.991637] SLOW spr round 41 (radius: 20) [06:38:13 -60974.991637] SLOW spr round 42 (radius: 25) [06:40:23] [worker #1] ML tree search #5, logLikelihood: -60923.994449 [06:47:39 -60974.991637] Model parameter optimization (eps = 0.100000) [06:48:01] [worker #0] ML tree search #7, logLikelihood: -60970.108576 [06:48:01 -135914.248128] Initial branch length optimization [06:48:04 -118333.514772] Model parameter optimization (eps = 10.000000) [06:48:42 -117730.207136] AUTODETECT spr round 1 (radius: 5) [06:51:07 -104178.525613] AUTODETECT spr round 2 (radius: 10) [06:54:12 -86022.314243] AUTODETECT spr round 3 (radius: 15) [06:57:51 -74195.314415] AUTODETECT spr round 4 (radius: 20) [07:01:55 -69947.291716] AUTODETECT spr round 5 (radius: 25) [07:06:52 -68777.390329] SPR radius for FAST iterations: 25 (autodetect) [07:06:52 -68777.390329] Model parameter optimization (eps = 3.000000) [07:07:18 -68700.339556] FAST spr round 1 (radius: 25) [07:11:33 -61866.960700] FAST spr round 2 (radius: 25) [07:14:28 -61145.494002] FAST spr round 3 (radius: 25) [07:17:00 -61065.787570] FAST spr round 4 (radius: 25) [07:19:17 -61045.737773] FAST spr round 5 (radius: 25) [07:21:21 -61042.473526] FAST spr round 6 (radius: 25) [07:23:21 -61036.215860] FAST spr round 7 (radius: 25) [07:25:18 -61035.285587] FAST spr round 8 (radius: 25) [07:25:56] [worker #2] ML tree search #9, logLikelihood: -60975.416395 [07:27:14 -61035.285505] Model parameter optimization (eps = 1.000000) [07:27:29 -61033.122860] SLOW spr round 1 (radius: 5) [07:30:03 -61006.677674] SLOW spr round 2 (radius: 5) [07:32:33 -60996.020337] SLOW spr round 3 (radius: 5) [07:35:02 -60991.285165] SLOW spr round 4 (radius: 5) [07:37:24 -60991.268961] SLOW spr round 5 (radius: 10) [07:39:51 -60988.763941] SLOW spr round 6 (radius: 5) [07:42:46 -60988.763877] SLOW spr round 7 (radius: 10) [07:45:30 -60987.613206] SLOW spr round 8 (radius: 5) [07:48:24 -60985.205394] SLOW spr round 9 (radius: 5) [07:50:59 -60985.205372] SLOW spr round 10 (radius: 10) [07:53:29 -60985.205372] SLOW spr round 11 (radius: 15) [07:58:00 -60984.055276] SLOW spr round 12 (radius: 5) [08:01:02 -60982.787031] SLOW spr round 13 (radius: 5) [08:03:43 -60982.787031] SLOW spr round 14 (radius: 10) [08:06:17 -60982.787031] SLOW spr round 15 (radius: 15) [08:10:43 -60982.787031] SLOW spr round 16 (radius: 20) [08:18:29 -60981.259943] SLOW spr round 17 (radius: 5) [08:21:33 -60981.259941] SLOW spr round 18 (radius: 10) [08:24:25 -60981.259941] SLOW spr round 19 (radius: 15) [08:27:50] [worker #1] ML tree search #8, logLikelihood: -61026.994417 [08:28:38 -60981.259941] SLOW spr round 20 (radius: 20) [08:36:35 -60981.259941] SLOW spr round 21 (radius: 25) [08:46:30 -60981.259941] Model parameter optimization (eps = 0.100000) [08:46:36] [worker #0] ML tree search #10, logLikelihood: -60981.253644 [08:46:36 -135242.684608] Initial branch length optimization [08:46:38 -117874.165446] Model parameter optimization (eps = 10.000000) [08:47:11 -117276.621459] AUTODETECT spr round 1 (radius: 5) [08:49:37 -103417.000676] AUTODETECT spr round 2 (radius: 10) [08:52:32 -86854.223523] AUTODETECT spr round 3 (radius: 15) [08:55:55 -76472.200662] AUTODETECT spr round 4 (radius: 20) [09:00:01 -70328.868567] AUTODETECT spr round 5 (radius: 25) [09:04:57 -68762.394761] SPR radius for FAST iterations: 25 (autodetect) [09:04:57 -68762.394761] Model parameter optimization (eps = 3.000000) [09:05:20 -68720.600266] FAST spr round 1 (radius: 25) [09:09:49 -61750.720243] FAST spr round 2 (radius: 25) [09:12:52 -61308.352465] FAST spr round 3 (radius: 25) [09:15:28 -61255.423939] FAST spr round 4 (radius: 25) [09:17:43 -61247.153273] FAST spr round 5 (radius: 25) [09:19:53 -61229.878333] FAST spr round 6 (radius: 25) [09:21:58 -61217.477241] FAST spr round 7 (radius: 25) [09:23:57 -61215.131540] FAST spr round 8 (radius: 25) [09:25:54 -61212.581860] FAST spr round 9 (radius: 25) [09:27:51 -61211.319154] FAST spr round 10 (radius: 25) [09:29:46 -61211.319150] Model parameter optimization (eps = 1.000000) [09:30:06 -61206.664751] SLOW spr round 1 (radius: 5) [09:32:48 -61177.157542] SLOW spr round 2 (radius: 5) [09:35:25 -61161.396115] SLOW spr round 3 (radius: 5) [09:37:50 -61161.395962] SLOW spr round 4 (radius: 10) [09:40:20 -61156.556010] SLOW spr round 5 (radius: 5) [09:43:24 -61152.399485] SLOW spr round 6 (radius: 5) [09:46:08 -61142.916867] SLOW spr round 7 (radius: 5) [09:48:38 -61142.045717] SLOW spr round 8 (radius: 5) [09:51:04 -61142.045709] SLOW spr round 9 (radius: 10) [09:53:31 -61139.825479] SLOW spr round 10 (radius: 5) [09:56:32 -61133.242121] SLOW spr round 11 (radius: 5) [09:59:13 -61132.067004] SLOW spr round 12 (radius: 5) [10:01:42 -61132.066899] SLOW spr round 13 (radius: 10) [10:04:02] [worker #2] ML tree search #12, logLikelihood: -60986.883134 [10:04:09 -61130.462614] SLOW spr round 14 (radius: 5) [10:07:05 -61130.462228] SLOW spr round 15 (radius: 10) [10:09:46 -61130.165479] SLOW spr round 16 (radius: 5) [10:12:39 -61130.139043] SLOW spr round 17 (radius: 10) [10:15:19 -61129.892912] SLOW spr round 18 (radius: 5) [10:18:16 -61128.589374] SLOW spr round 19 (radius: 5) [10:20:53 -61128.589264] SLOW spr round 20 (radius: 10) [10:23:23 -61128.542016] SLOW spr round 21 (radius: 15) [10:28:02 -61126.938257] SLOW spr round 22 (radius: 5) [10:31:05 -61126.609398] SLOW spr round 23 (radius: 5) [10:33:45 -61126.609275] SLOW spr round 24 (radius: 10) [10:36:18 -61126.609267] SLOW spr round 25 (radius: 15) [10:40:55 -61125.607857] SLOW spr round 26 (radius: 5) [10:43:55 -61125.607846] SLOW spr round 27 (radius: 10) [10:46:41 -61125.607846] SLOW spr round 28 (radius: 15) [10:51:03 -61125.513405] SLOW spr round 29 (radius: 20) [10:58:45 -61099.601620] SLOW spr round 30 (radius: 5) [11:01:52 -61055.186984] SLOW spr round 31 (radius: 5) [11:04:34 -61055.168456] SLOW spr round 32 (radius: 10) [11:07:07 -61055.168236] SLOW spr round 33 (radius: 15) [11:11:38 -61055.168232] SLOW spr round 34 (radius: 20) [11:17:17] [worker #2] ML tree search #15, logLikelihood: -61009.938893 [11:19:06 -61054.789272] SLOW spr round 35 (radius: 5) [11:22:16 -61036.133127] SLOW spr round 36 (radius: 5) [11:25:02 -61032.678672] SLOW spr round 37 (radius: 5) [11:27:33 -61032.651167] SLOW spr round 38 (radius: 10) [11:30:01 -61029.126752] SLOW spr round 39 (radius: 5) [11:32:59 -61028.435422] SLOW spr round 40 (radius: 5) [11:35:38 -61028.348005] SLOW spr round 41 (radius: 10) [11:38:07 -61028.347993] SLOW spr round 42 (radius: 15) [11:42:33 -61028.347993] SLOW spr round 43 (radius: 20) [11:49:34 -61022.852011] SLOW spr round 44 (radius: 5) [11:52:42 -60961.833913] SLOW spr round 45 (radius: 5) [11:55:27 -60958.232697] SLOW spr round 46 (radius: 5) [11:57:59 -60958.232639] SLOW spr round 47 (radius: 10) [12:00:25 -60958.232639] SLOW spr round 48 (radius: 15) [12:04:44 -60958.232639] SLOW spr round 49 (radius: 20) [12:11:24 -60958.232639] SLOW spr round 50 (radius: 25) [12:11:39] [worker #1] ML tree search #11, logLikelihood: -60933.680205 [12:20:01 -60957.180816] SLOW spr round 51 (radius: 5) [12:23:04 -60957.180800] SLOW spr round 52 (radius: 10) [12:25:52 -60957.180799] SLOW spr round 53 (radius: 15) [12:29:45 -60957.180799] SLOW spr round 54 (radius: 20) [12:36:30 -60955.490026] SLOW spr round 55 (radius: 5) [12:39:32 -60955.489931] SLOW spr round 56 (radius: 10) [12:42:17 -60955.489927] SLOW spr round 57 (radius: 15) [12:46:12 -60955.489926] SLOW spr round 58 (radius: 20) [12:53:00 -60955.489926] SLOW spr round 59 (radius: 25) [13:01:33 -60955.489926] Model parameter optimization (eps = 0.100000) [13:01:47] [worker #0] ML tree search #13, logLikelihood: -60954.743017 [13:01:47 -135511.876284] Initial branch length optimization [13:01:49 -118335.354125] Model parameter optimization (eps = 10.000000) [13:02:26 -117751.801055] AUTODETECT spr round 1 (radius: 5) [13:04:51 -105075.499461] AUTODETECT spr round 2 (radius: 10) [13:07:48 -87471.916068] AUTODETECT spr round 3 (radius: 15) [13:11:11 -75177.478188] AUTODETECT spr round 4 (radius: 20) [13:15:37 -70659.548446] AUTODETECT spr round 5 (radius: 25) [13:21:02 -69123.657130] SPR radius for FAST iterations: 25 (autodetect) [13:21:02 -69123.657130] Model parameter optimization (eps = 3.000000) [13:21:23 -69089.766949] FAST spr round 1 (radius: 25) [13:25:39 -61982.258151] FAST spr round 2 (radius: 25) [13:28:41 -61166.254295] FAST spr round 3 (radius: 25) [13:31:17 -61091.161970] FAST spr round 4 (radius: 25) [13:33:33 -61074.713451] FAST spr round 5 (radius: 25) [13:35:37 -61071.337767] FAST spr round 6 (radius: 25) [13:37:35 -61071.337744] Model parameter optimization (eps = 1.000000) [13:37:45 -61070.524236] SLOW spr round 1 (radius: 5) [13:40:26 -61046.659109] SLOW spr round 2 (radius: 5) [13:42:59 -61036.391320] SLOW spr round 3 (radius: 5) [13:45:26 -61036.390607] SLOW spr round 4 (radius: 10) [13:47:56 -61034.564894] SLOW spr round 5 (radius: 5) [13:50:55 -61034.563990] SLOW spr round 6 (radius: 10) [13:53:40 -61034.520787] SLOW spr round 7 (radius: 15) [13:58:10 -61034.520628] SLOW spr round 8 (radius: 20) [14:05:59 -61034.520608] SLOW spr round 9 (radius: 25) [14:13:50] [worker #1] ML tree search #14, logLikelihood: -60987.872584 [14:15:43 -61027.049195] SLOW spr round 10 (radius: 5) [14:18:53 -61024.650740] SLOW spr round 11 (radius: 5) [14:21:44 -61019.598086] SLOW spr round 12 (radius: 5) [14:24:23 -61015.589651] SLOW spr round 13 (radius: 5) [14:26:56 -61014.239622] SLOW spr round 14 (radius: 5) [14:29:23 -61013.426180] SLOW spr round 15 (radius: 5) [14:31:46 -61013.426122] SLOW spr round 16 (radius: 10) [14:34:14 -61013.426122] SLOW spr round 17 (radius: 15) [14:36:38] [worker #2] ML tree search #18, logLikelihood: -60950.675524 [14:39:01 -61013.426122] SLOW spr round 18 (radius: 20) [14:46:52 -61012.845688] SLOW spr round 19 (radius: 5) [14:50:13 -61012.174086] SLOW spr round 20 (radius: 5) [14:53:13 -61012.174085] SLOW spr round 21 (radius: 10) [14:56:01 -61012.174085] SLOW spr round 22 (radius: 15) [15:00:48 -61011.794058] SLOW spr round 23 (radius: 5) [15:04:07 -61011.794039] SLOW spr round 24 (radius: 10) [15:07:08 -61011.794039] SLOW spr round 25 (radius: 15) [15:11:44 -61011.794039] SLOW spr round 26 (radius: 20) [15:19:59 -61011.794039] SLOW spr round 27 (radius: 25) [15:30:05 -61009.557691] SLOW spr round 28 (radius: 5) [15:33:30 -61009.338842] SLOW spr round 29 (radius: 5) [15:36:32 -61009.333267] SLOW spr round 30 (radius: 10) [15:39:15 -61008.843040] SLOW spr round 31 (radius: 5) [15:42:27 -61008.723907] SLOW spr round 32 (radius: 5) [15:45:20 -61008.723803] SLOW spr round 33 (radius: 10) [15:48:01 -61008.388805] SLOW spr round 34 (radius: 5) [15:51:13 -61008.387504] SLOW spr round 35 (radius: 10) [15:54:11 -61008.387504] SLOW spr round 36 (radius: 15) [15:58:23 -61008.387504] SLOW spr round 37 (radius: 20) [16:05:52 -61008.387504] SLOW spr round 38 (radius: 25) [16:15:40 -61008.387504] Model parameter optimization (eps = 0.100000) [16:15:53] [worker #0] ML tree search #16, logLikelihood: -61007.901582 [16:15:53 -135009.009952] Initial branch length optimization [16:15:55 -118179.172781] Model parameter optimization (eps = 10.000000) [16:16:24 -117633.533769] AUTODETECT spr round 1 (radius: 5) [16:18:42 -104209.880050] AUTODETECT spr round 2 (radius: 10) [16:21:34 -88428.188137] AUTODETECT spr round 3 (radius: 15) [16:25:07 -75373.041179] AUTODETECT spr round 4 (radius: 20) [16:30:07 -70041.484084] AUTODETECT spr round 5 (radius: 25) [16:35:54 -69393.875217] SPR radius for FAST iterations: 25 (autodetect) [16:35:54 -69393.875217] Model parameter optimization (eps = 3.000000) [16:36:17 -69340.575448] FAST spr round 1 (radius: 25) [16:40:58 -61805.365560] FAST spr round 2 (radius: 25) [16:43:57 -61134.858565] FAST spr round 3 (radius: 25) [16:46:26 -61054.030592] FAST spr round 4 (radius: 25) [16:48:36 -61049.215886] FAST spr round 5 (radius: 25) [16:49:22] [worker #1] ML tree search #17, logLikelihood: -60959.954007 [16:50:35 -61049.214217] Model parameter optimization (eps = 1.000000) [16:50:57 -61043.428848] SLOW spr round 1 (radius: 5) [16:53:33 -61030.343794] SLOW spr round 2 (radius: 5) [16:56:04 -61017.821467] SLOW spr round 3 (radius: 5) [16:58:27 -61017.513531] SLOW spr round 4 (radius: 5) [17:00:45 -61017.513461] SLOW spr round 5 (radius: 10) [17:03:11 -61015.835766] SLOW spr round 6 (radius: 5) [17:06:10 -61000.268306] SLOW spr round 7 (radius: 5) [17:08:49 -60997.774267] SLOW spr round 8 (radius: 5) [17:11:16 -60997.774077] SLOW spr round 9 (radius: 10) [17:13:43 -60997.087539] SLOW spr round 10 (radius: 5) [17:16:37 -60996.972402] SLOW spr round 11 (radius: 5) [17:19:14 -60996.972290] SLOW spr round 12 (radius: 10) [17:21:44 -60996.972282] SLOW spr round 13 (radius: 15) [17:26:34 -60996.972281] SLOW spr round 14 (radius: 20) [17:34:49 -60994.072380] SLOW spr round 15 (radius: 5) [17:37:54 -60987.835744] SLOW spr round 16 (radius: 5) [17:40:36 -60987.833767] SLOW spr round 17 (radius: 10) [17:43:10 -60987.688558] SLOW spr round 18 (radius: 5) [17:46:07 -60984.831164] SLOW spr round 19 (radius: 5) [17:48:43 -60984.831104] SLOW spr round 20 (radius: 10) [17:51:13 -60984.831104] SLOW spr round 21 (radius: 15) [17:55:53 -60984.831104] SLOW spr round 22 (radius: 20) [18:03:43 -60984.831104] SLOW spr round 23 (radius: 25) [18:13:29 -60984.831104] Model parameter optimization (eps = 0.100000) [18:13:41] [worker #0] ML tree search #19, logLikelihood: -60984.717043 [19:29:41] [worker #1] ML tree search #20, logLikelihood: -60981.526963 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.237235,0.371133) (0.143774,0.784060) (0.406930,0.706489) (0.212061,2.413155) 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: -60923.994449 AIC score: 125857.988899 / AICc score: 8169917.988899 / BIC score: 131727.132537 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=138). 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/P01763/3_mltree/P01763.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/3_mltree/P01763.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/3_mltree/P01763.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P01763/3_mltree/P01763.raxml.log Analysis started: 03-Jul-2021 07:53:39 / finished: 04-Jul-2021 03:23:22 Elapsed time: 70182.063 seconds Consumed energy: 6253.304 Wh (= 31 km in an electric car, or 156 km with an e-scooter!)