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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 01-Jul-2021 09:42:34 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/2_msa/Q9H930_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/2_msa/Q9H930_trimmed_msa.fasta
[00:00:00] Loaded alignment with 793 taxa and 783 sites

WARNING: Sequences tr_A0A2R8RZL6_A0A2R8RZL6_DANRE_7955 and tr_X1WDS1_X1WDS1_DANRE_7955 are exactly identical!
WARNING: Sequences tr_H2N6A8_H2N6A8_PONAB_9601 and tr_H2PZQ4_H2PZQ4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A087ZS71_A0A087ZS71_APIME_7460 and tr_A0A2A3EPJ8_A0A2A3EPJ8_APICC_94128 are exactly identical!
WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_F6VVE4_F6VVE4_MACMU_9544 are exactly identical!
WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2K5LKM0_A0A2K5LKM0_CERAT_9531 are exactly identical!
WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2K6DBD8_A0A2K6DBD8_MACNE_9545 are exactly identical!
WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2R8ZN70_A0A2R8ZN70_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1P6BSD2_A0A1P6BSD2_BRUMA_6279 and tr_A0A0N4TJ75_A0A0N4TJ75_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A044SY86_A0A044SY86_ONCVO_6282 and tr_A0A182EIB6_A0A182EIB6_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A2I3MNS3_A0A2I3MNS3_PAPAN_9555 and tr_A0A2K5KQB3_A0A2K5KQB3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9S688_A0A0D9S688_CHLSB_60711 and tr_A0A2K6CNS5_A0A2K6CNS5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2D0RV48_A0A2D0RV48_ICTPU_7998 and tr_A0A2D0RWP1_A0A2D0RWP1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4CGU1_A0A2U4CGU1_TURTR_9739 and tr_A0A2Y9NPI3_A0A2Y9NPI3_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 13

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.reduced.phy

Alignment comprises 1 partitions and 783 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 783 / 783
Gaps: 42.58 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 793 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -824325.979945] Initial branch length optimization
[00:00:36 -682066.494269] Model parameter optimization (eps = 10.000000)
[00:16:06 -679193.928936] AUTODETECT spr round 1 (radius: 5)
[00:24:37 -481223.208973] AUTODETECT spr round 2 (radius: 10)
[00:28:52 -375006.307453] AUTODETECT spr round 3 (radius: 15)
[00:36:02 -311757.034648] AUTODETECT spr round 4 (radius: 20)
[00:50:34 -297105.798149] AUTODETECT spr round 5 (radius: 25)
[01:18:38 -282430.278664] SPR radius for FAST iterations: 25 (autodetect)
[01:18:39 -282430.278664] Model parameter optimization (eps = 3.000000)
[01:25:26 -281865.009647] FAST spr round 1 (radius: 25)
[01:36:03 -250525.739051] FAST spr round 2 (radius: 25)
[01:40:18 -249218.970079] FAST spr round 3 (radius: 25)
[01:46:45 -249103.910682] FAST spr round 4 (radius: 25)
[01:49:53 -249097.028102] FAST spr round 5 (radius: 25)
[01:52:29 -249097.016191] Model parameter optimization (eps = 1.000000)
[01:53:10 -249060.940477] SLOW spr round 1 (radius: 5)
[02:06:39 -249017.444542] SLOW spr round 2 (radius: 5)
[02:12:02 -249010.274002] SLOW spr round 3 (radius: 5)
[02:15:56 -249008.141146] SLOW spr round 4 (radius: 5)
[02:18:33 -249008.140850] SLOW spr round 5 (radius: 10)
[02:21:39 -249006.911757] SLOW spr round 6 (radius: 5)
[02:28:10 -249006.907177] SLOW spr round 7 (radius: 10)
[02:39:17 -249006.907157] SLOW spr round 8 (radius: 15)
[02:53:28 -249006.907138] SLOW spr round 9 (radius: 20)
[03:12:35 -249006.907119] SLOW spr round 10 (radius: 25)
[03:45:51 -249006.907100] Model parameter optimization (eps = 0.100000)

[03:46:17] [worker #0] ML tree search #1, logLikelihood: -249006.816454

[03:46:17 -830959.771370] Initial branch length optimization
[03:46:33 -684006.591654] Model parameter optimization (eps = 10.000000)
[03:48:51 -681277.006330] AUTODETECT spr round 1 (radius: 5)
[03:54:20] [worker #1] ML tree search #2, logLikelihood: -248967.926763
[03:54:27 -500855.294390] AUTODETECT spr round 2 (radius: 10)
[04:02:22 -359392.961386] AUTODETECT spr round 3 (radius: 15)
[04:10:54 -307008.831282] AUTODETECT spr round 4 (radius: 20)
[04:19:39 -287382.191507] AUTODETECT spr round 5 (radius: 25)
[04:33:54 -281602.983380] SPR radius for FAST iterations: 25 (autodetect)
[04:33:54 -281602.983380] Model parameter optimization (eps = 3.000000)
[04:36:51 -281005.048996] FAST spr round 1 (radius: 25)
[04:47:28 -250396.717406] FAST spr round 2 (radius: 25)
[05:00:37 -249185.864042] FAST spr round 3 (radius: 25)
[05:06:10 -249105.580628] FAST spr round 4 (radius: 25)
[05:10:23 -249089.734276] FAST spr round 5 (radius: 25)
[05:14:14 -249088.332552] FAST spr round 6 (radius: 25)
[05:21:37 -249088.332269] Model parameter optimization (eps = 1.000000)
[05:25:07 -249057.168746] SLOW spr round 1 (radius: 5)
[05:32:26 -249013.875721] SLOW spr round 2 (radius: 5)
[05:39:05 -249002.922360] SLOW spr round 3 (radius: 5)
[05:45:07 -249002.024026] SLOW spr round 4 (radius: 5)
[05:50:41 -249002.022341] SLOW spr round 5 (radius: 10)
[06:06:22 -248989.825893] SLOW spr round 6 (radius: 5)
[06:36:11 -248982.720323] SLOW spr round 7 (radius: 5)
[06:43:47 -248982.720024] SLOW spr round 8 (radius: 10)
[06:49:30 -248982.534747] SLOW spr round 9 (radius: 5)
[06:52:42 -248973.894053] SLOW spr round 10 (radius: 5)
[06:58:58 -248973.893785] SLOW spr round 11 (radius: 10)
[07:01:05 -248973.893765] SLOW spr round 12 (radius: 15)
[07:09:44 -248973.893758] SLOW spr round 13 (radius: 20)
[07:20:19 -248973.893751] SLOW spr round 14 (radius: 25)
[07:43:59 -248973.893745] Model parameter optimization (eps = 0.100000)

[07:44:21] [worker #0] ML tree search #3, logLikelihood: -248973.779604

[07:44:22 -821506.961797] Initial branch length optimization
[08:00:13 -677985.285626] Model parameter optimization (eps = 10.000000)
[08:08:12 -675198.598053] AUTODETECT spr round 1 (radius: 5)
[08:20:24 -488661.960104] AUTODETECT spr round 2 (radius: 10)
[08:45:24 -365106.873577] AUTODETECT spr round 3 (radius: 15)
[08:54:28 -315927.683138] AUTODETECT spr round 4 (radius: 20)
[09:08:00 -288414.122590] AUTODETECT spr round 5 (radius: 25)
[09:16:11] [worker #1] ML tree search #4, logLikelihood: -248978.205097
[09:21:11 -284605.964901] SPR radius for FAST iterations: 25 (autodetect)
[09:21:11 -284605.964901] Model parameter optimization (eps = 3.000000)
[09:23:32 -284117.586005] FAST spr round 1 (radius: 25)
[09:32:34 -250954.683841] FAST spr round 2 (radius: 25)
[09:38:51 -249188.106805] FAST spr round 3 (radius: 25)
[09:43:57 -249109.142527] FAST spr round 4 (radius: 25)
[09:48:13 -249083.725911] FAST spr round 5 (radius: 25)
[09:51:55 -249075.580634] FAST spr round 6 (radius: 25)
[09:54:20 -249075.576809] Model parameter optimization (eps = 1.000000)
[09:55:02 -249039.705010] SLOW spr round 1 (radius: 5)
[10:03:48 -248973.512935] SLOW spr round 2 (radius: 5)
[10:10:54 -248969.480839] SLOW spr round 3 (radius: 5)
[10:16:11 -248968.644900] SLOW spr round 4 (radius: 5)
[10:19:48 -248968.644784] SLOW spr round 5 (radius: 10)
[10:30:38 -248968.644708] SLOW spr round 6 (radius: 15)
[10:41:01 -248968.644642] SLOW spr round 7 (radius: 20)
[10:57:03 -248968.644585] SLOW spr round 8 (radius: 25)
[11:08:34 -248968.644534] Model parameter optimization (eps = 0.100000)

[11:09:23] [worker #0] ML tree search #5, logLikelihood: -248968.549862

[11:09:23 -827404.038106] Initial branch length optimization
[11:18:57 -686672.906093] Model parameter optimization (eps = 10.000000)
[11:29:00 -683752.612392] AUTODETECT spr round 1 (radius: 5)
[11:45:29 -496319.745945] AUTODETECT spr round 2 (radius: 10)
[12:01:36 -370166.591715] AUTODETECT spr round 3 (radius: 15)
[12:15:37 -314731.128488] AUTODETECT spr round 4 (radius: 20)
[12:24:08 -292214.686369] AUTODETECT spr round 5 (radius: 25)
[12:49:25 -285461.561555] SPR radius for FAST iterations: 25 (autodetect)
[12:49:25 -285461.561555] Model parameter optimization (eps = 3.000000)
[12:55:09 -284829.933821] FAST spr round 1 (radius: 25)
[13:15:49 -250295.534123] FAST spr round 2 (radius: 25)
[13:23:40 -249171.658286] FAST spr round 3 (radius: 25)
[13:28:54 -249072.315187] FAST spr round 4 (radius: 25)
[13:48:36 -249071.698988] FAST spr round 5 (radius: 25)
[13:52:23 -249071.687218] Model parameter optimization (eps = 1.000000)
[13:53:10 -249057.911067] SLOW spr round 1 (radius: 5)
[14:21:39 -248994.910223] SLOW spr round 2 (radius: 5)
[14:43:54] [worker #1] ML tree search #6, logLikelihood: -248960.384527
[14:53:53 -248993.320954] SLOW spr round 3 (radius: 5)
[15:22:31 -248993.044198] SLOW spr round 4 (radius: 5)
[15:49:22 -248991.231456] SLOW spr round 5 (radius: 5)
[16:29:15 -248991.231397] SLOW spr round 6 (radius: 10)
[16:59:23] [worker #1] ML tree search #8, logLikelihood: -248980.790914
[17:03:09 -248991.231350] SLOW spr round 7 (radius: 15)
[17:16:11 -248990.589292] SLOW spr round 8 (radius: 5)
[17:29:12 -248990.589256] SLOW spr round 9 (radius: 10)
[17:56:16 -248990.589217] SLOW spr round 10 (radius: 15)
[18:06:21 -248990.589183] SLOW spr round 11 (radius: 20)
[18:23:14 -248990.589151] SLOW spr round 12 (radius: 25)
[18:45:46 -248990.589120] Model parameter optimization (eps = 0.100000)

[18:45:59] [worker #0] ML tree search #7, logLikelihood: -248990.549807

[18:46:00 -819711.355570] Initial branch length optimization
[18:53:40 -680822.489682] Model parameter optimization (eps = 10.000000)
[19:02:36 -677957.096842] AUTODETECT spr round 1 (radius: 5)
[19:57:43 -478993.928061] AUTODETECT spr round 2 (radius: 10)
[20:03:59 -353302.673127] AUTODETECT spr round 3 (radius: 15)
[20:14:39 -292910.809177] AUTODETECT spr round 4 (radius: 20)
[20:24:58 -277934.037637] AUTODETECT spr round 5 (radius: 25)
[20:37:52 -274186.485828] SPR radius for FAST iterations: 25 (autodetect)
[20:37:52 -274186.485828] Model parameter optimization (eps = 3.000000)
[20:39:16 -273647.330332] FAST spr round 1 (radius: 25)
[20:48:06 -250027.711317] FAST spr round 2 (radius: 25)
[20:54:30 -249154.009434] FAST spr round 3 (radius: 25)
[21:01:23 -249065.151506] FAST spr round 4 (radius: 25)
[21:06:24 -249054.766219] FAST spr round 5 (radius: 25)
[21:25:34] [worker #1] ML tree search #10, logLikelihood: -248981.653618
[21:26:41 -249054.765882] Model parameter optimization (eps = 1.000000)
[21:27:40 -249025.050888] SLOW spr round 1 (radius: 5)
[21:33:31 -248964.920497] SLOW spr round 2 (radius: 5)
[21:38:03 -248957.576387] SLOW spr round 3 (radius: 5)
[21:41:28 -248957.575996] SLOW spr round 4 (radius: 10)
[21:45:43 -248956.933301] SLOW spr round 5 (radius: 5)
[21:48:51 -248956.933286] SLOW spr round 6 (radius: 10)
[21:51:58 -248956.933169] SLOW spr round 7 (radius: 15)
[21:59:49 -248956.933156] SLOW spr round 8 (radius: 20)
[22:17:09 -248956.933143] SLOW spr round 9 (radius: 25)
[22:38:41 -248956.933131] Model parameter optimization (eps = 0.100000)

[22:38:57] [worker #0] ML tree search #9, logLikelihood: -248956.895500

[22:38:57 -829258.109135] Initial branch length optimization
[22:49:04 -687805.498604] Model parameter optimization (eps = 10.000000)
[22:50:59 -684818.121608] AUTODETECT spr round 1 (radius: 5)
[22:54:51 -508294.035124] AUTODETECT spr round 2 (radius: 10)
[22:59:46 -370879.406683] AUTODETECT spr round 3 (radius: 15)
[23:06:18 -318631.903725] AUTODETECT spr round 4 (radius: 20)
[23:15:41 -292038.693351] AUTODETECT spr round 5 (radius: 25)
[23:59:44 -282699.435189] SPR radius for FAST iterations: 25 (autodetect)
[23:59:45 -282699.435189] Model parameter optimization (eps = 3.000000)
[24:00:56 -282059.616889] FAST spr round 1 (radius: 25)
[24:13:24 -250513.641512] FAST spr round 2 (radius: 25)
[25:15:33 -249155.491672] FAST spr round 3 (radius: 25)
[25:29:03 -249086.839909] FAST spr round 4 (radius: 25)
[25:32:54 -249085.580631] FAST spr round 5 (radius: 25)
[25:35:40 -249085.579641] Model parameter optimization (eps = 1.000000)
[25:36:20 -249051.614218] SLOW spr round 1 (radius: 5)
[25:42:05 -248985.642930] SLOW spr round 2 (radius: 5)
[25:45:05 -248979.443626] SLOW spr round 3 (radius: 5)
[25:49:48 -248979.443469] SLOW spr round 4 (radius: 10)
[25:54:34 -248979.443390] SLOW spr round 5 (radius: 15)
[26:06:27 -248979.443321] SLOW spr round 6 (radius: 20)
[26:23:28 -248979.443259] SLOW spr round 7 (radius: 25)
[26:31:38 -248979.443201] Model parameter optimization (eps = 0.100000)

[26:32:02] [worker #0] ML tree search #11, logLikelihood: -248979.063286

[26:32:02 -823743.340064] Initial branch length optimization
[26:32:43 -680035.328903] Model parameter optimization (eps = 10.000000)
[26:35:05 -677271.674542] AUTODETECT spr round 1 (radius: 5)
[26:40:43 -488292.276221] AUTODETECT spr round 2 (radius: 10)
[26:46:57 -355682.446226] AUTODETECT spr round 3 (radius: 15)
[26:54:25 -288385.589650] AUTODETECT spr round 4 (radius: 20)
[27:03:08 -278112.274707] AUTODETECT spr round 5 (radius: 25)
[27:14:31 -277530.098812] SPR radius for FAST iterations: 25 (autodetect)
[27:14:31 -277530.098812] Model parameter optimization (eps = 3.000000)
[27:16:00 -276962.191180] FAST spr round 1 (radius: 25)
[27:17:47] [worker #1] ML tree search #12, logLikelihood: -248982.293630
[27:23:42 -250544.780202] FAST spr round 2 (radius: 25)
[27:32:31 -249291.502831] FAST spr round 3 (radius: 25)
[27:36:06 -249124.759415] FAST spr round 4 (radius: 25)
[27:39:44 -249081.874913] FAST spr round 5 (radius: 25)
[27:43:15 -249064.237717] FAST spr round 6 (radius: 25)
[27:46:05 -249064.237662] Model parameter optimization (eps = 1.000000)
[27:46:42 -249039.383169] SLOW spr round 1 (radius: 5)
[27:49:00 -248989.692275] SLOW spr round 2 (radius: 5)
[27:52:03 -248974.479360] SLOW spr round 3 (radius: 5)
[28:28:57 -248970.675893] SLOW spr round 4 (radius: 5)
[28:34:32 -248970.306760] SLOW spr round 5 (radius: 5)
[28:39:59 -248970.306714] SLOW spr round 6 (radius: 10)
[28:45:30 -248969.503616] SLOW spr round 7 (radius: 5)
[28:52:14 -248969.503567] SLOW spr round 8 (radius: 10)
[28:58:26 -248969.503555] SLOW spr round 9 (radius: 15)
[29:08:38 -248969.503544] SLOW spr round 10 (radius: 20)
[29:27:24 -248969.503535] SLOW spr round 11 (radius: 25)
[29:52:27 -248969.503526] Model parameter optimization (eps = 0.100000)

[29:52:50] [worker #0] ML tree search #13, logLikelihood: -248969.362243

[29:52:51 -824134.149349] Initial branch length optimization
[29:53:36 -686291.751335] Model parameter optimization (eps = 10.000000)
[29:55:10 -683570.095002] AUTODETECT spr round 1 (radius: 5)
[30:00:43 -504462.624948] AUTODETECT spr round 2 (radius: 10)
[30:09:55 -374182.319401] AUTODETECT spr round 3 (radius: 15)
[30:48:40 -302474.780828] AUTODETECT spr round 4 (radius: 20)
[31:08:10 -283468.002695] AUTODETECT spr round 5 (radius: 25)
[31:19:44 -277865.734007] SPR radius for FAST iterations: 25 (autodetect)
[31:19:44 -277865.734007] Model parameter optimization (eps = 3.000000)
[31:26:58 -277369.112303] FAST spr round 1 (radius: 25)
[31:35:42 -250227.837839] FAST spr round 2 (radius: 25)
[31:41:35 -249111.617696] FAST spr round 3 (radius: 25)
[31:46:18 -249073.230388] FAST spr round 4 (radius: 25)
[32:05:03] [worker #1] ML tree search #14, logLikelihood: -248977.563696
[32:17:06 -249069.370754] FAST spr round 5 (radius: 25)
[32:20:57 -249069.368879] Model parameter optimization (eps = 1.000000)
[32:21:49 -249036.836002] SLOW spr round 1 (radius: 5)
[32:31:59 -248984.638267] SLOW spr round 2 (radius: 5)
[32:37:33 -248983.372360] SLOW spr round 3 (radius: 5)
[32:42:51 -248983.370309] SLOW spr round 4 (radius: 10)
[32:48:24 -248981.440273] SLOW spr round 5 (radius: 5)
[32:51:22 -248977.498573] SLOW spr round 6 (radius: 5)
[33:01:57 -248973.826683] SLOW spr round 7 (radius: 5)
[33:14:16 -248973.826322] SLOW spr round 8 (radius: 10)
[33:19:51 -248973.826206] SLOW spr round 9 (radius: 15)
[33:31:02 -248973.826105] SLOW spr round 10 (radius: 20)
[33:52:25 -248973.826017] SLOW spr round 11 (radius: 25)
[34:18:59 -248973.825939] Model parameter optimization (eps = 0.100000)

[34:23:13] [worker #0] ML tree search #15, logLikelihood: -248973.697650

[34:23:13 -820743.177125] Initial branch length optimization
[34:24:20 -685803.163193] Model parameter optimization (eps = 10.000000)
[34:28:56 -682977.748091] AUTODETECT spr round 1 (radius: 5)
[34:35:25 -490303.998574] AUTODETECT spr round 2 (radius: 10)
[34:51:20 -349667.874202] AUTODETECT spr round 3 (radius: 15)
[36:01:39 -295452.245457] AUTODETECT spr round 4 (radius: 20)
[36:15:25 -279837.431338] AUTODETECT spr round 5 (radius: 25)
[36:24:25 -278465.285076] SPR radius for FAST iterations: 25 (autodetect)
[36:24:25 -278465.285076] Model parameter optimization (eps = 3.000000)
[36:26:44 -277843.951323] FAST spr round 1 (radius: 25)
[36:38:21] [worker #1] ML tree search #16, logLikelihood: -248967.235583
[38:31:13 -250363.217048] FAST spr round 2 (radius: 25)
[38:33:28 -249187.328158] FAST spr round 3 (radius: 25)
[38:35:19 -249074.967367] FAST spr round 4 (radius: 25)
[38:36:52 -249069.212467] FAST spr round 5 (radius: 25)
[38:38:18 -249065.326671] FAST spr round 6 (radius: 25)
[38:39:42 -249065.324558] Model parameter optimization (eps = 1.000000)
[38:40:04 -249030.714980] SLOW spr round 1 (radius: 5)
[38:42:19 -248976.104364] SLOW spr round 2 (radius: 5)
[38:45:05] [worker #1] ML tree search #18, logLikelihood: -248987.269755
[38:45:40 -248970.765208] SLOW spr round 3 (radius: 5)
[38:57:11 -248970.764839] SLOW spr round 4 (radius: 10)
[39:00:57 -248970.764815] SLOW spr round 5 (radius: 15)
[39:07:33 -248970.122091] SLOW spr round 6 (radius: 5)
[39:11:23 -248970.121906] SLOW spr round 7 (radius: 10)
[39:15:09 -248968.819771] SLOW spr round 8 (radius: 5)
[39:18:09 -248966.923250] SLOW spr round 9 (radius: 5)
[39:21:19 -248966.922771] SLOW spr round 10 (radius: 10)
[39:25:51 -248966.922620] SLOW spr round 11 (radius: 15)
[39:31:08 -248966.922610] SLOW spr round 12 (radius: 20)
[39:41:04 -248966.922602] SLOW spr round 13 (radius: 25)
[39:51:17] [worker #1] ML tree search #20, logLikelihood: -249005.004340
[40:04:03 -248966.922595] Model parameter optimization (eps = 0.100000)

[40:04:09] [worker #0] ML tree search #17, logLikelihood: -248966.864729

[40:04:09 -825450.397237] Initial branch length optimization
[40:04:15 -683847.688707] Model parameter optimization (eps = 10.000000)
[40:05:22 -681104.305701] AUTODETECT spr round 1 (radius: 5)
[40:07:20 -490580.108222] AUTODETECT spr round 2 (radius: 10)
[41:58:49 -368820.175543] AUTODETECT spr round 3 (radius: 15)
[42:01:17 -328366.692187] AUTODETECT spr round 4 (radius: 20)
[42:04:16 -296959.330992] AUTODETECT spr round 5 (radius: 25)
[42:08:34 -288982.245481] SPR radius for FAST iterations: 25 (autodetect)
[42:08:34 -288982.245481] Model parameter optimization (eps = 3.000000)
[42:09:10 -288276.145085] FAST spr round 1 (radius: 25)
[42:12:15 -250565.502350] FAST spr round 2 (radius: 25)
[42:14:29 -249162.673262] FAST spr round 3 (radius: 25)
[42:16:20 -249055.467615] FAST spr round 4 (radius: 25)
[42:17:53 -249051.892849] FAST spr round 5 (radius: 25)
[42:19:19 -249051.255257] FAST spr round 6 (radius: 25)
[42:20:45 -249051.254826] Model parameter optimization (eps = 1.000000)
[42:21:05 -249029.762000] SLOW spr round 1 (radius: 5)
[42:23:21 -248965.753300] SLOW spr round 2 (radius: 5)
[42:25:27 -248964.665152] SLOW spr round 3 (radius: 5)
[42:27:28 -248964.664672] SLOW spr round 4 (radius: 10)
[42:29:30 -248964.021865] SLOW spr round 5 (radius: 5)
[42:32:09 -248964.021776] SLOW spr round 6 (radius: 10)
[42:34:35 -248964.021598] SLOW spr round 7 (radius: 15)
[42:38:27 -248964.021532] SLOW spr round 8 (radius: 20)
[42:44:54 -248964.021474] SLOW spr round 9 (radius: 25)
[42:53:03 -248964.021423] Model parameter optimization (eps = 0.100000)

[42:53:16] [worker #0] ML tree search #19, logLikelihood: -248963.966672


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.103912,0.609792) (0.034570,1.036254) (0.290830,0.670641) (0.570688,1.236699) 
   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: -248956.895500

AIC score: 501091.790999 / AICc score: 5554111.790999 / BIC score: 508501.508853
Free parameters (model + branch lengths): 1589

WARNING: Number of free parameters (K=1589) is larger than alignment size (n=783).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H930/3_mltree/Q9H930.raxml.log

Analysis started: 01-Jul-2021 09:42:34 / finished: 03-Jul-2021 04:35:51

Elapsed time: 154396.727 seconds