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 04-Jul-2021 19:02:12 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/2_msa/Q8IXW0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/2_msa/Q8IXW0_trimmed_msa.fasta [00:00:00] Loaded alignment with 58 taxa and 613 sites Alignment comprises 1 partitions and 610 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 613 / 610 Gaps: 20.24 % Invariant sites: 3.75 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 58 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 88 / 7040 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -47043.018666] Initial branch length optimization [00:00:00 -40116.145559] Model parameter optimization (eps = 10.000000) [00:00:03 -39813.470240] AUTODETECT spr round 1 (radius: 5) [00:00:04 -29683.537443] AUTODETECT spr round 2 (radius: 10) [00:00:05 -27828.504290] AUTODETECT spr round 3 (radius: 15) [00:00:06 -27828.483145] SPR radius for FAST iterations: 10 (autodetect) [00:00:06 -27828.483145] Model parameter optimization (eps = 3.000000) [00:00:08 -27596.153771] FAST spr round 1 (radius: 10) [00:00:10 -26960.496054] FAST spr round 2 (radius: 10) [00:00:11 -26945.699098] FAST spr round 3 (radius: 10) [00:00:12 -26942.899875] FAST spr round 4 (radius: 10) [00:00:13 -26942.391089] FAST spr round 5 (radius: 10) [00:00:14 -26942.388586] Model parameter optimization (eps = 1.000000) [00:00:15 -26941.255866] SLOW spr round 1 (radius: 5) [00:00:17 -26936.151802] SLOW spr round 2 (radius: 5) [00:00:20 -26935.963988] SLOW spr round 3 (radius: 5) [00:00:22 -26935.962737] SLOW spr round 4 (radius: 10) [00:00:25 -26935.962687] SLOW spr round 5 (radius: 15) [00:00:28 -26935.962684] SLOW spr round 6 (radius: 20) [00:00:29 -26935.962684] SLOW spr round 7 (radius: 25) [00:00:29 -26935.962684] Model parameter optimization (eps = 0.100000) [00:00:30] ML tree search #1, logLikelihood: -26935.912409 [00:00:30 -46651.363750] Initial branch length optimization [00:00:30 -39694.518450] Model parameter optimization (eps = 10.000000) [00:00:32 -39520.139273] AUTODETECT spr round 1 (radius: 5) [00:00:33 -29610.611128] AUTODETECT spr round 2 (radius: 10) [00:00:34 -28140.692958] AUTODETECT spr round 3 (radius: 15) [00:00:35 -28140.685287] SPR radius for FAST iterations: 10 (autodetect) [00:00:35 -28140.685287] Model parameter optimization (eps = 3.000000) [00:00:37 -28045.782077] FAST spr round 1 (radius: 10) [00:00:38 -27190.217414] FAST spr round 2 (radius: 10) [00:00:39 -26945.881710] FAST spr round 3 (radius: 10) [00:00:40 -26942.602973] FAST spr round 4 (radius: 10) [00:00:41 -26941.134903] FAST spr round 5 (radius: 10) [00:00:42 -26940.121509] FAST spr round 6 (radius: 10) [00:00:44 -26939.129451] FAST spr round 7 (radius: 10) [00:00:45 -26938.258093] FAST spr round 8 (radius: 10) [00:00:46 -26937.851287] FAST spr round 9 (radius: 10) [00:00:47 -26937.846383] Model parameter optimization (eps = 1.000000) [00:00:48 -26935.913247] SLOW spr round 1 (radius: 5) [00:00:50 -26935.912423] SLOW spr round 2 (radius: 10) [00:00:53 -26935.912397] SLOW spr round 3 (radius: 15) [00:00:56 -26935.912395] SLOW spr round 4 (radius: 20) [00:00:57 -26935.912395] SLOW spr round 5 (radius: 25) [00:00:58 -26935.912395] Model parameter optimization (eps = 0.100000) [00:00:58] ML tree search #2, logLikelihood: -26935.912368 [00:00:58 -45703.105749] Initial branch length optimization [00:00:58 -39622.744599] Model parameter optimization (eps = 10.000000) [00:01:00 -39442.838525] AUTODETECT spr round 1 (radius: 5) [00:01:01 -29946.808953] AUTODETECT spr round 2 (radius: 10) [00:01:02 -27969.548983] AUTODETECT spr round 3 (radius: 15) [00:01:03 -27969.533553] SPR radius for FAST iterations: 10 (autodetect) [00:01:03 -27969.533553] Model parameter optimization (eps = 3.000000) [00:01:05 -27913.509611] FAST spr round 1 (radius: 10) [00:01:06 -26956.403582] FAST spr round 2 (radius: 10) [00:01:07 -26947.118887] FAST spr round 3 (radius: 10) [00:01:09 -26942.591072] FAST spr round 4 (radius: 10) [00:01:10 -26939.910682] FAST spr round 5 (radius: 10) [00:01:11 -26939.011701] FAST spr round 6 (radius: 10) [00:01:12 -26939.011670] Model parameter optimization (eps = 1.000000) [00:01:13 -26936.416953] SLOW spr round 1 (radius: 5) [00:01:15 -26935.944410] SLOW spr round 2 (radius: 5) [00:01:18 -26935.944322] SLOW spr round 3 (radius: 10) [00:01:20 -26935.944319] SLOW spr round 4 (radius: 15) [00:01:23 -26935.944319] SLOW spr round 5 (radius: 20) [00:01:24 -26935.944319] SLOW spr round 6 (radius: 25) [00:01:25 -26935.944319] Model parameter optimization (eps = 0.100000) [00:01:25] ML tree search #3, logLikelihood: -26935.912738 [00:01:25 -46594.690938] Initial branch length optimization [00:01:25 -39561.299448] Model parameter optimization (eps = 10.000000) [00:01:28 -39394.628648] AUTODETECT spr round 1 (radius: 5) [00:01:28 -29072.624633] AUTODETECT spr round 2 (radius: 10) [00:01:29 -28079.280538] AUTODETECT spr round 3 (radius: 15) [00:01:30 -28079.271332] SPR radius for FAST iterations: 10 (autodetect) [00:01:30 -28079.271332] Model parameter optimization (eps = 3.000000) [00:01:32 -27962.840628] FAST spr round 1 (radius: 10) [00:01:34 -26960.357414] FAST spr round 2 (radius: 10) [00:01:35 -26944.063047] FAST spr round 3 (radius: 10) [00:01:36 -26940.742479] FAST spr round 4 (radius: 10) [00:01:37 -26939.196413] FAST spr round 5 (radius: 10) [00:01:38 -26937.669880] FAST spr round 6 (radius: 10) [00:01:39 -26937.083513] FAST spr round 7 (radius: 10) [00:01:40 -26936.994936] Model parameter optimization (eps = 1.000000) [00:01:41 -26935.923467] SLOW spr round 1 (radius: 5) [00:01:43 -26935.912838] SLOW spr round 2 (radius: 10) [00:01:46 -26935.912446] SLOW spr round 3 (radius: 15) [00:01:49 -26935.912404] SLOW spr round 4 (radius: 20) [00:01:50 -26935.912399] SLOW spr round 5 (radius: 25) [00:01:50 -26935.912398] Model parameter optimization (eps = 0.100000) [00:01:50] ML tree search #4, logLikelihood: -26935.912385 [00:01:50 -46353.522493] Initial branch length optimization [00:01:51 -39263.696982] Model parameter optimization (eps = 10.000000) [00:01:53 -39038.701150] AUTODETECT spr round 1 (radius: 5) [00:01:54 -30776.462959] AUTODETECT spr round 2 (radius: 10) [00:01:55 -28015.050607] AUTODETECT spr round 3 (radius: 15) [00:01:56 -27948.626875] AUTODETECT spr round 4 (radius: 20) [00:01:56 -27948.624100] SPR radius for FAST iterations: 15 (autodetect) [00:01:56 -27948.624100] Model parameter optimization (eps = 3.000000) [00:01:58 -27868.088705] FAST spr round 1 (radius: 15) [00:02:00 -26982.693887] FAST spr round 2 (radius: 15) [00:02:01 -26948.410182] FAST spr round 3 (radius: 15) [00:02:02 -26943.506860] FAST spr round 4 (radius: 15) [00:02:03 -26942.616830] FAST spr round 5 (radius: 15) [00:02:04 -26941.283658] FAST spr round 6 (radius: 15) [00:02:05 -26940.504983] FAST spr round 7 (radius: 15) [00:02:06 -26940.504940] Model parameter optimization (eps = 1.000000) [00:02:07 -26936.417104] SLOW spr round 1 (radius: 5) [00:02:10 -26935.945260] SLOW spr round 2 (radius: 5) [00:02:12 -26935.945001] SLOW spr round 3 (radius: 10) [00:02:14 -26935.944992] SLOW spr round 4 (radius: 15) [00:02:17 -26935.944992] SLOW spr round 5 (radius: 20) [00:02:19 -26935.944992] SLOW spr round 6 (radius: 25) [00:02:19 -26935.944992] Model parameter optimization (eps = 0.100000) [00:02:20] ML tree search #5, logLikelihood: -26935.912754 [00:02:20 -45766.922179] Initial branch length optimization [00:02:20 -39697.270489] Model parameter optimization (eps = 10.000000) [00:02:22 -39406.797847] AUTODETECT spr round 1 (radius: 5) [00:02:23 -30639.746020] AUTODETECT spr round 2 (radius: 10) [00:02:24 -28366.430393] AUTODETECT spr round 3 (radius: 15) [00:02:25 -28366.411550] SPR radius for FAST iterations: 10 (autodetect) [00:02:25 -28366.411550] Model parameter optimization (eps = 3.000000) [00:02:27 -28266.475323] FAST spr round 1 (radius: 10) [00:02:29 -26948.507588] FAST spr round 2 (radius: 10) [00:02:30 -26944.629774] FAST spr round 3 (radius: 10) [00:02:31 -26940.916899] FAST spr round 4 (radius: 10) [00:02:32 -26940.783491] FAST spr round 5 (radius: 10) [00:02:33 -26940.783202] Model parameter optimization (eps = 1.000000) [00:02:34 -26936.418314] SLOW spr round 1 (radius: 5) [00:02:37 -26935.946033] SLOW spr round 2 (radius: 5) [00:02:39 -26935.945764] SLOW spr round 3 (radius: 10) [00:02:41 -26935.945753] SLOW spr round 4 (radius: 15) [00:02:44 -26935.945753] SLOW spr round 5 (radius: 20) [00:02:46 -26935.945753] SLOW spr round 6 (radius: 25) [00:02:46 -26935.945753] Model parameter optimization (eps = 0.100000) [00:02:47] ML tree search #6, logLikelihood: -26935.912761 [00:02:47 -45956.521172] Initial branch length optimization [00:02:47 -38734.108048] Model parameter optimization (eps = 10.000000) [00:02:48 -38565.694376] AUTODETECT spr round 1 (radius: 5) [00:02:49 -30911.279496] AUTODETECT spr round 2 (radius: 10) [00:02:50 -28087.862018] AUTODETECT spr round 3 (radius: 15) [00:02:51 -28087.841986] SPR radius for FAST iterations: 10 (autodetect) [00:02:51 -28087.841986] Model parameter optimization (eps = 3.000000) [00:02:53 -28000.890842] FAST spr round 1 (radius: 10) [00:02:55 -26984.016534] FAST spr round 2 (radius: 10) [00:02:56 -26938.668416] FAST spr round 3 (radius: 10) [00:02:57 -26938.041007] FAST spr round 4 (radius: 10) [00:02:58 -26937.956072] Model parameter optimization (eps = 1.000000) [00:02:59 -26936.120169] SLOW spr round 1 (radius: 5) [00:03:02 -26935.938289] SLOW spr round 2 (radius: 5) [00:03:04 -26935.926981] SLOW spr round 3 (radius: 10) [00:03:06 -26935.926810] SLOW spr round 4 (radius: 15) [00:03:09 -26935.926790] SLOW spr round 5 (radius: 20) [00:03:11 -26935.926788] SLOW spr round 6 (radius: 25) [00:03:11 -26935.926788] Model parameter optimization (eps = 0.100000) [00:03:12] ML tree search #7, logLikelihood: -26935.912399 [00:03:12 -45525.432664] Initial branch length optimization [00:03:12 -38834.449980] Model parameter optimization (eps = 10.000000) [00:03:14 -38639.117186] AUTODETECT spr round 1 (radius: 5) [00:03:15 -29478.874210] AUTODETECT spr round 2 (radius: 10) [00:03:16 -27534.892087] AUTODETECT spr round 3 (radius: 15) [00:03:17 -27534.885148] SPR radius for FAST iterations: 10 (autodetect) [00:03:17 -27534.885148] Model parameter optimization (eps = 3.000000) [00:03:19 -27400.416350] FAST spr round 1 (radius: 10) [00:03:20 -26941.471083] FAST spr round 2 (radius: 10) [00:03:21 -26936.900739] FAST spr round 3 (radius: 10) [00:03:22 -26936.686578] FAST spr round 4 (radius: 10) [00:03:23 -26936.458459] FAST spr round 5 (radius: 10) [00:03:24 -26936.456779] Model parameter optimization (eps = 1.000000) [00:03:25 -26935.953370] SLOW spr round 1 (radius: 5) [00:03:27 -26935.918179] SLOW spr round 2 (radius: 10) [00:03:30 -26935.917878] SLOW spr round 3 (radius: 15) [00:03:33 -26935.917842] SLOW spr round 4 (radius: 20) [00:03:34 -26935.917838] SLOW spr round 5 (radius: 25) [00:03:35 -26935.917838] Model parameter optimization (eps = 0.100000) [00:03:35] ML tree search #8, logLikelihood: -26935.912425 [00:03:35 -47476.931269] Initial branch length optimization [00:03:35 -40061.761180] Model parameter optimization (eps = 10.000000) [00:03:38 -39865.205707] AUTODETECT spr round 1 (radius: 5) [00:03:38 -29466.887248] AUTODETECT spr round 2 (radius: 10) [00:03:40 -28194.531152] AUTODETECT spr round 3 (radius: 15) [00:03:41 -28194.524226] SPR radius for FAST iterations: 10 (autodetect) [00:03:41 -28194.524226] Model parameter optimization (eps = 3.000000) [00:03:42 -28101.379140] FAST spr round 1 (radius: 10) [00:03:44 -26964.078381] FAST spr round 2 (radius: 10) [00:03:45 -26958.062988] FAST spr round 3 (radius: 10) [00:03:46 -26954.911101] FAST spr round 4 (radius: 10) [00:03:47 -26948.942887] FAST spr round 5 (radius: 10) [00:03:48 -26945.994568] FAST spr round 6 (radius: 10) [00:03:49 -26941.167161] FAST spr round 7 (radius: 10) [00:03:50 -26939.755144] FAST spr round 8 (radius: 10) [00:03:52 -26938.434975] FAST spr round 9 (radius: 10) [00:03:53 -26937.855109] FAST spr round 10 (radius: 10) [00:03:54 -26937.852852] Model parameter optimization (eps = 1.000000) [00:03:55 -26936.119885] SLOW spr round 1 (radius: 5) [00:03:57 -26935.926944] SLOW spr round 2 (radius: 5) [00:03:59 -26935.925569] SLOW spr round 3 (radius: 10) [00:04:02 -26935.925514] SLOW spr round 4 (radius: 15) [00:04:05 -26935.925510] SLOW spr round 5 (radius: 20) [00:04:06 -26935.925510] SLOW spr round 6 (radius: 25) [00:04:07 -26935.925510] Model parameter optimization (eps = 0.100000) [00:04:07] ML tree search #9, logLikelihood: -26935.912393 [00:04:07 -46356.669889] Initial branch length optimization [00:04:07 -39838.404415] Model parameter optimization (eps = 10.000000) [00:04:09 -39678.377378] AUTODETECT spr round 1 (radius: 5) [00:04:10 -29004.749421] AUTODETECT spr round 2 (radius: 10) [00:04:11 -27775.752584] AUTODETECT spr round 3 (radius: 15) [00:04:12 -27775.748897] SPR radius for FAST iterations: 10 (autodetect) [00:04:12 -27775.748897] Model parameter optimization (eps = 3.000000) [00:04:14 -27715.067035] FAST spr round 1 (radius: 10) [00:04:15 -26975.116927] FAST spr round 2 (radius: 10) [00:04:16 -26958.382084] FAST spr round 3 (radius: 10) [00:04:17 -26948.042094] FAST spr round 4 (radius: 10) [00:04:18 -26945.707342] FAST spr round 5 (radius: 10) [00:04:20 -26944.192822] FAST spr round 6 (radius: 10) [00:04:21 -26943.284149] FAST spr round 7 (radius: 10) [00:04:22 -26942.689949] FAST spr round 8 (radius: 10) [00:04:23 -26942.118952] FAST spr round 9 (radius: 10) [00:04:24 -26941.520709] FAST spr round 10 (radius: 10) [00:04:25 -26938.036569] FAST spr round 11 (radius: 10) [00:04:26 -26937.647304] FAST spr round 12 (radius: 10) [00:04:27 -26937.646672] Model parameter optimization (eps = 1.000000) [00:04:27 -26936.428654] SLOW spr round 1 (radius: 5) [00:04:30 -26935.942970] SLOW spr round 2 (radius: 5) [00:04:32 -26935.942629] SLOW spr round 3 (radius: 10) [00:04:35 -26935.942616] SLOW spr round 4 (radius: 15) [00:04:38 -26935.942615] SLOW spr round 5 (radius: 20) [00:04:39 -26935.942615] SLOW spr round 6 (radius: 25) [00:04:40 -26935.942615] Model parameter optimization (eps = 0.100000) [00:04:40] ML tree search #10, logLikelihood: -26935.912742 [00:04:40 -46021.661342] Initial branch length optimization [00:04:40 -39241.522073] Model parameter optimization (eps = 10.000000) [00:04:42 -39052.842062] AUTODETECT spr round 1 (radius: 5) [00:04:43 -29768.783694] AUTODETECT spr round 2 (radius: 10) [00:04:44 -27916.601934] AUTODETECT spr round 3 (radius: 15) [00:04:44 -27886.818835] AUTODETECT spr round 4 (radius: 20) [00:04:45 -27886.810578] SPR radius for FAST iterations: 15 (autodetect) [00:04:45 -27886.810578] Model parameter optimization (eps = 3.000000) [00:04:47 -27783.203358] FAST spr round 1 (radius: 15) [00:04:49 -26973.702868] FAST spr round 2 (radius: 15) [00:04:50 -26963.546827] FAST spr round 3 (radius: 15) [00:04:51 -26947.597917] FAST spr round 4 (radius: 15) [00:04:52 -26943.291103] FAST spr round 5 (radius: 15) [00:04:53 -26940.343215] FAST spr round 6 (radius: 15) [00:04:54 -26938.930332] FAST spr round 7 (radius: 15) [00:04:55 -26938.023637] FAST spr round 8 (radius: 15) [00:04:56 -26937.597995] FAST spr round 9 (radius: 15) [00:04:57 -26937.563737] Model parameter optimization (eps = 1.000000) [00:04:58 -26936.111452] SLOW spr round 1 (radius: 5) [00:05:00 -26935.927128] SLOW spr round 2 (radius: 5) [00:05:03 -26935.925919] SLOW spr round 3 (radius: 10) [00:05:05 -26935.925874] SLOW spr round 4 (radius: 15) [00:05:08 -26935.925872] SLOW spr round 5 (radius: 20) [00:05:10 -26935.925871] SLOW spr round 6 (radius: 25) [00:05:10 -26935.925871] Model parameter optimization (eps = 0.100000) [00:05:10] ML tree search #11, logLikelihood: -26935.912398 [00:05:10 -45851.843137] Initial branch length optimization [00:05:11 -39529.655400] Model parameter optimization (eps = 10.000000) [00:05:13 -39282.647003] AUTODETECT spr round 1 (radius: 5) [00:05:14 -29941.815133] AUTODETECT spr round 2 (radius: 10) [00:05:15 -27483.430944] AUTODETECT spr round 3 (radius: 15) [00:05:16 -27483.415452] SPR radius for FAST iterations: 10 (autodetect) [00:05:16 -27483.415452] Model parameter optimization (eps = 3.000000) [00:05:18 -27406.907118] FAST spr round 1 (radius: 10) [00:05:19 -26965.705945] FAST spr round 2 (radius: 10) [00:05:20 -26946.845388] FAST spr round 3 (radius: 10) [00:05:21 -26942.437449] FAST spr round 4 (radius: 10) [00:05:23 -26939.086909] FAST spr round 5 (radius: 10) [00:05:24 -26937.713124] FAST spr round 6 (radius: 10) [00:05:25 -26937.106474] FAST spr round 7 (radius: 10) [00:05:26 -26937.010872] Model parameter optimization (eps = 1.000000) [00:05:27 -26935.913122] SLOW spr round 1 (radius: 5) [00:05:29 -26935.912539] SLOW spr round 2 (radius: 10) [00:05:32 -26935.912527] SLOW spr round 3 (radius: 15) [00:05:35 -26935.912526] SLOW spr round 4 (radius: 20) [00:05:36 -26935.912526] SLOW spr round 5 (radius: 25) [00:05:36 -26935.912526] Model parameter optimization (eps = 0.100000) [00:05:37] ML tree search #12, logLikelihood: -26935.912386 [00:05:37 -46461.081477] Initial branch length optimization [00:05:37 -39446.038383] Model parameter optimization (eps = 10.000000) [00:05:39 -39220.390967] AUTODETECT spr round 1 (radius: 5) [00:05:39 -28302.368026] AUTODETECT spr round 2 (radius: 10) [00:05:41 -27918.436736] AUTODETECT spr round 3 (radius: 15) [00:05:42 -27918.432862] SPR radius for FAST iterations: 10 (autodetect) [00:05:42 -27918.432862] Model parameter optimization (eps = 3.000000) [00:05:43 -27822.818566] FAST spr round 1 (radius: 10) [00:05:45 -26971.392225] FAST spr round 2 (radius: 10) [00:05:46 -26947.528567] FAST spr round 3 (radius: 10) [00:05:47 -26945.518825] FAST spr round 4 (radius: 10) [00:05:48 -26944.174196] FAST spr round 5 (radius: 10) [00:05:49 -26940.415679] FAST spr round 6 (radius: 10) [00:05:50 -26939.064999] FAST spr round 7 (radius: 10) [00:05:51 -26938.639759] FAST spr round 8 (radius: 10) [00:05:52 -26938.639171] Model parameter optimization (eps = 1.000000) [00:05:53 -26936.429564] SLOW spr round 1 (radius: 5) [00:05:56 -26935.947145] SLOW spr round 2 (radius: 5) [00:05:58 -26935.946797] SLOW spr round 3 (radius: 10) [00:06:01 -26935.946779] SLOW spr round 4 (radius: 15) [00:06:04 -26935.946778] SLOW spr round 5 (radius: 20) [00:06:05 -26935.946778] SLOW spr round 6 (radius: 25) [00:06:05 -26935.946778] Model parameter optimization (eps = 0.100000) [00:06:06] ML tree search #13, logLikelihood: -26935.912786 [00:06:06 -46317.462540] Initial branch length optimization [00:06:06 -39446.811050] Model parameter optimization (eps = 10.000000) [00:06:09 -39252.389669] AUTODETECT spr round 1 (radius: 5) [00:06:09 -30303.142519] AUTODETECT spr round 2 (radius: 10) [00:06:11 -27583.930151] AUTODETECT spr round 3 (radius: 15) [00:06:11 -27583.924343] SPR radius for FAST iterations: 10 (autodetect) [00:06:11 -27583.924343] Model parameter optimization (eps = 3.000000) [00:06:14 -27489.977227] FAST spr round 1 (radius: 10) [00:06:15 -26939.133102] FAST spr round 2 (radius: 10) [00:06:16 -26937.819499] FAST spr round 3 (radius: 10) [00:06:17 -26937.256333] FAST spr round 4 (radius: 10) [00:06:18 -26937.063540] FAST spr round 5 (radius: 10) [00:06:20 -26937.063190] Model parameter optimization (eps = 1.000000) [00:06:20 -26936.420896] SLOW spr round 1 (radius: 5) [00:06:23 -26935.960581] SLOW spr round 2 (radius: 5) [00:06:25 -26935.960289] SLOW spr round 3 (radius: 10) [00:06:27 -26935.960280] SLOW spr round 4 (radius: 15) [00:06:30 -26935.960279] SLOW spr round 5 (radius: 20) [00:06:32 -26935.960279] SLOW spr round 6 (radius: 25) [00:06:32 -26935.960279] Model parameter optimization (eps = 0.100000) [00:06:33] ML tree search #14, logLikelihood: -26935.913129 [00:06:33 -46627.619697] Initial branch length optimization [00:06:33 -39843.991719] Model parameter optimization (eps = 10.000000) [00:06:36 -39644.920714] AUTODETECT spr round 1 (radius: 5) [00:06:37 -29819.600346] AUTODETECT spr round 2 (radius: 10) [00:06:38 -28312.632078] AUTODETECT spr round 3 (radius: 15) [00:06:39 -28312.619370] SPR radius for FAST iterations: 10 (autodetect) [00:06:39 -28312.619370] Model parameter optimization (eps = 3.000000) [00:06:40 -28187.044628] FAST spr round 1 (radius: 10) [00:06:42 -26952.497804] FAST spr round 2 (radius: 10) [00:06:43 -26938.512568] FAST spr round 3 (radius: 10) [00:06:44 -26937.979491] FAST spr round 4 (radius: 10) [00:06:45 -26937.555623] FAST spr round 5 (radius: 10) [00:06:46 -26937.338298] FAST spr round 6 (radius: 10) [00:06:47 -26937.337924] Model parameter optimization (eps = 1.000000) [00:06:48 -26936.420644] SLOW spr round 1 (radius: 5) [00:06:50 -26935.959090] SLOW spr round 2 (radius: 5) [00:06:53 -26935.958766] SLOW spr round 3 (radius: 10) [00:06:55 -26935.958756] SLOW spr round 4 (radius: 15) [00:06:58 -26935.958755] SLOW spr round 5 (radius: 20) [00:07:00 -26935.958755] SLOW spr round 6 (radius: 25) [00:07:00 -26935.958755] Model parameter optimization (eps = 0.100000) [00:07:00] ML tree search #15, logLikelihood: -26935.913019 [00:07:00 -46402.239773] Initial branch length optimization [00:07:00 -39201.032123] Model parameter optimization (eps = 10.000000) [00:07:02 -39015.807490] AUTODETECT spr round 1 (radius: 5) [00:07:03 -31001.837958] AUTODETECT spr round 2 (radius: 10) [00:07:04 -27629.510097] AUTODETECT spr round 3 (radius: 15) [00:07:05 -27626.374348] AUTODETECT spr round 4 (radius: 20) [00:07:05 -27626.365330] SPR radius for FAST iterations: 15 (autodetect) [00:07:05 -27626.365330] Model parameter optimization (eps = 3.000000) [00:07:07 -27555.067955] FAST spr round 1 (radius: 15) [00:07:08 -26950.327029] FAST spr round 2 (radius: 15) [00:07:09 -26947.274731] FAST spr round 3 (radius: 15) [00:07:10 -26941.273685] FAST spr round 4 (radius: 15) [00:07:11 -26939.746043] FAST spr round 5 (radius: 15) [00:07:13 -26938.636963] FAST spr round 6 (radius: 15) [00:07:14 -26938.042316] FAST spr round 7 (radius: 15) [00:07:15 -26937.941155] FAST spr round 8 (radius: 15) [00:07:16 -26937.914702] Model parameter optimization (eps = 1.000000) [00:07:17 -26935.952352] SLOW spr round 1 (radius: 5) [00:07:19 -26935.915556] SLOW spr round 2 (radius: 10) [00:07:22 -26935.915194] SLOW spr round 3 (radius: 15) [00:07:25 -26935.915153] SLOW spr round 4 (radius: 20) [00:07:26 -26935.915148] SLOW spr round 5 (radius: 25) [00:07:27 -26935.915147] Model parameter optimization (eps = 0.100000) [00:07:27] ML tree search #16, logLikelihood: -26935.912360 [00:07:27 -46593.121294] Initial branch length optimization [00:07:27 -39791.415875] Model parameter optimization (eps = 10.000000) [00:07:29 -39602.069720] AUTODETECT spr round 1 (radius: 5) [00:07:30 -30012.025970] AUTODETECT spr round 2 (radius: 10) [00:07:31 -27829.888234] AUTODETECT spr round 3 (radius: 15) [00:07:32 -27829.852034] SPR radius for FAST iterations: 10 (autodetect) [00:07:32 -27829.852034] Model parameter optimization (eps = 3.000000) [00:07:34 -27726.658717] FAST spr round 1 (radius: 10) [00:07:36 -26977.914219] FAST spr round 2 (radius: 10) [00:07:37 -26950.472590] FAST spr round 3 (radius: 10) [00:07:38 -26946.276226] FAST spr round 4 (radius: 10) [00:07:39 -26944.614617] FAST spr round 5 (radius: 10) [00:07:40 -26941.763062] FAST spr round 6 (radius: 10) [00:07:41 -26940.060605] FAST spr round 7 (radius: 10) [00:07:42 -26939.127764] FAST spr round 8 (radius: 10) [00:07:43 -26938.595028] FAST spr round 9 (radius: 10) [00:07:44 -26938.345443] FAST spr round 10 (radius: 10) [00:07:45 -26938.344040] Model parameter optimization (eps = 1.000000) [00:07:47 -26935.952243] SLOW spr round 1 (radius: 5) [00:07:49 -26935.915610] SLOW spr round 2 (radius: 10) [00:07:51 -26935.915337] SLOW spr round 3 (radius: 15) [00:07:54 -26935.915304] SLOW spr round 4 (radius: 20) [00:07:56 -26935.915300] SLOW spr round 5 (radius: 25) [00:07:56 -26935.915299] Model parameter optimization (eps = 0.100000) [00:07:57] ML tree search #17, logLikelihood: -26935.912342 [00:07:57 -45601.878818] Initial branch length optimization [00:07:57 -39194.517422] Model parameter optimization (eps = 10.000000) [00:07:58 -38912.921462] AUTODETECT spr round 1 (radius: 5) [00:07:59 -28922.892381] AUTODETECT spr round 2 (radius: 10) [00:08:00 -27805.872133] AUTODETECT spr round 3 (radius: 15) [00:08:01 -27805.856400] SPR radius for FAST iterations: 10 (autodetect) [00:08:01 -27805.856400] Model parameter optimization (eps = 3.000000) [00:08:03 -27626.387599] FAST spr round 1 (radius: 10) [00:08:05 -26964.126965] FAST spr round 2 (radius: 10) [00:08:06 -26944.787291] FAST spr round 3 (radius: 10) [00:08:07 -26941.156962] FAST spr round 4 (radius: 10) [00:08:08 -26938.486225] FAST spr round 5 (radius: 10) [00:08:09 -26937.375103] FAST spr round 6 (radius: 10) [00:08:10 -26937.036078] FAST spr round 7 (radius: 10) [00:08:11 -26937.030961] Model parameter optimization (eps = 1.000000) [00:08:12 -26935.951508] SLOW spr round 1 (radius: 5) [00:08:14 -26935.916154] SLOW spr round 2 (radius: 10) [00:08:17 -26935.915812] SLOW spr round 3 (radius: 15) [00:08:20 -26935.915771] SLOW spr round 4 (radius: 20) [00:08:21 -26935.915766] SLOW spr round 5 (radius: 25) [00:08:22 -26935.915766] Model parameter optimization (eps = 0.100000) [00:08:22] ML tree search #18, logLikelihood: -26935.912361 [00:08:22 -45370.514197] Initial branch length optimization [00:08:22 -38663.330370] Model parameter optimization (eps = 10.000000) [00:08:24 -38483.013913] AUTODETECT spr round 1 (radius: 5) [00:08:24 -30289.786448] AUTODETECT spr round 2 (radius: 10) [00:08:26 -27695.162267] AUTODETECT spr round 3 (radius: 15) [00:08:27 -27637.295775] AUTODETECT spr round 4 (radius: 20) [00:08:27 -27637.274456] SPR radius for FAST iterations: 15 (autodetect) [00:08:27 -27637.274456] Model parameter optimization (eps = 3.000000) [00:08:29 -27581.191084] FAST spr round 1 (radius: 15) [00:08:30 -26975.221320] FAST spr round 2 (radius: 15) [00:08:32 -26951.109307] FAST spr round 3 (radius: 15) [00:08:33 -26940.790469] FAST spr round 4 (radius: 15) [00:08:34 -26936.939406] FAST spr round 5 (radius: 15) [00:08:35 -26936.811039] FAST spr round 6 (radius: 15) [00:08:36 -26936.810754] Model parameter optimization (eps = 1.000000) [00:08:36 -26935.915071] SLOW spr round 1 (radius: 5) [00:08:39 -26935.913316] SLOW spr round 2 (radius: 10) [00:08:41 -26935.913287] SLOW spr round 3 (radius: 15) [00:08:44 -26935.913286] SLOW spr round 4 (radius: 20) [00:08:46 -26935.913286] SLOW spr round 5 (radius: 25) [00:08:46 -26935.913286] Model parameter optimization (eps = 0.100000) [00:08:46] ML tree search #19, logLikelihood: -26935.912478 [00:08:46 -45910.246718] Initial branch length optimization [00:08:46 -38752.424225] Model parameter optimization (eps = 10.000000) [00:08:49 -38555.350922] AUTODETECT spr round 1 (radius: 5) [00:08:49 -29585.868840] AUTODETECT spr round 2 (radius: 10) [00:08:50 -28002.978244] AUTODETECT spr round 3 (radius: 15) [00:08:51 -27992.430525] AUTODETECT spr round 4 (radius: 20) [00:08:52 -27992.428310] SPR radius for FAST iterations: 15 (autodetect) [00:08:52 -27992.428310] Model parameter optimization (eps = 3.000000) [00:08:54 -27890.004977] FAST spr round 1 (radius: 15) [00:08:55 -26997.098450] FAST spr round 2 (radius: 15) [00:08:56 -26949.568055] FAST spr round 3 (radius: 15) [00:08:57 -26944.788456] FAST spr round 4 (radius: 15) [00:08:59 -26943.368107] FAST spr round 5 (radius: 15) [00:09:00 -26942.809406] FAST spr round 6 (radius: 15) [00:09:01 -26942.494720] FAST spr round 7 (radius: 15) [00:09:02 -26942.254357] FAST spr round 8 (radius: 15) [00:09:03 -26942.253963] Model parameter optimization (eps = 1.000000) [00:09:04 -26936.416358] SLOW spr round 1 (radius: 5) [00:09:06 -26935.944016] SLOW spr round 2 (radius: 5) [00:09:09 -26935.943734] SLOW spr round 3 (radius: 10) [00:09:11 -26935.943725] SLOW spr round 4 (radius: 15) [00:09:14 -26935.943724] SLOW spr round 5 (radius: 20) [00:09:16 -26935.943724] SLOW spr round 6 (radius: 25) [00:09:16 -26935.943724] Model parameter optimization (eps = 0.100000) [00:09:16] ML tree search #20, logLikelihood: -26935.912772 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.174355,0.474997) (0.079592,0.958822) (0.341341,0.637479) (0.404712,1.540031) 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: -26935.912342 AIC score: 54109.824684 / AICc score: 54167.755718 / BIC score: 54635.610111 Free parameters (model + branch lengths): 119 Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IXW0/3_mltree/Q8IXW0.raxml.log Analysis started: 04-Jul-2021 19:02:12 / finished: 04-Jul-2021 19:11:29 Elapsed time: 556.842 seconds Consumed energy: 48.364 Wh