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 05-Jul-2021 11:46:31 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/2_msa/Q8TAQ2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/3_mltree/Q8TAQ2 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/2_msa/Q8TAQ2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 503 sites

WARNING: Sequences tr_A0A2R8RV42_A0A2R8RV42_DANRE_7955 and tr_E7FFZ4_E7FFZ4_DANRE_7955 are exactly identical!
WARNING: Sequences tr_D8RD88_D8RD88_SELML_88036 and tr_D8RSG6_D8RSG6_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3S0V2_G3S0V2_GORGO_9595 and tr_A0A2I3T0A7_A0A2I3T0A7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S0V2_G3S0V2_GORGO_9595 and sp_Q8TAQ2_SMRC2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S0V2_G3S0V2_GORGO_9595 and tr_F6PUJ0_F6PUJ0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3S0V2_G3S0V2_GORGO_9595 and tr_A0A2R8ZZS5_A0A2R8ZZS5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q296N7_Q296N7_DROPS_46245 and tr_B4GEW6_B4GEW6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A179US86_A0A179US86_BLAGS_559298 and tr_C5GDV1_C5GDV1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_E2REF0_E2REF0_CANLF_9615 and tr_A0A2Y9IYK8_A0A2Y9IYK8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_H2QMI4_H2QMI4_PANTR_9598 and sp_Q92922_SMRC1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6UZL9_F6UZL9_HORSE_9796 and tr_G1M390_G1M390_AILME_9646 are exactly identical!
WARNING: Sequences tr_F7HJJ3_F7HJJ3_MACMU_9544 and tr_A0A2K6E0R0_A0A2K6E0R0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XGP3_G7XGP3_ASPKW_1033177 and tr_A0A146F049_A0A146F049_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XGP3_G7XGP3_ASPKW_1033177 and tr_A0A317URG0_A0A317URG0_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F4WR49_F4WR49_ACREC_103372 and tr_A0A195FKT0_A0A195FKT0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_E6R7E7_E6R7E7_CRYGW_367775 and tr_A0A095CGE0_A0A095CGE0_CRYGR_294750 are exactly identical!
WARNING: Sequences tr_G2Y3C7_G2Y3C7_BOTF4_999810 and tr_M7U645_M7U645_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A8XGN4_A8XGN4_CAEBR_6238 and tr_A0A2G5TTE2_A0A2G5TTE2_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A0A0D2XJU2_A0A0D2XJU2_FUSO4_426428 and tr_N4U2U2_N4U2U2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2XJU2_A0A0D2XJU2_FUSO4_426428 and tr_X0CB09_X0CB09_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XJU2_A0A0D2XJU2_FUSO4_426428 and tr_A0A2H3T139_A0A2H3T139_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_L0P9G7_L0P9G7_PNEJ8_1209962 and tr_A0A0W4ZIM8_A0A0W4ZIM8_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_A0A015KSL9_A0A015KSL9_9GLOM_1432141 and tr_A0A2I1HIB4_A0A2I1HIB4_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015KSL9_A0A015KSL9_9GLOM_1432141 and tr_U9U1T5_U9U1T5_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A094EGZ3_A0A094EGZ3_9PEZI_1420912 and tr_A0A1B8GCZ0_A0A1B8GCZ0_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0A1NXB1_A0A0A1NXB1_9FUNG_58291 and tr_A0A367J2G1_A0A367J2G1_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1NZD3_A0A0A1NZD3_9FUNG_58291 and tr_A0A367JZ62_A0A367JZ62_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0VRL3_A0A0V0VRL3_9BILA_181606 and tr_A0A0V1P7G9_A0A0V1P7G9_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A100IF98_A0A100IF98_ASPNG_5061 and tr_A0A1L9MXL9_A0A1L9MXL9_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_I1RE51_I1RE51_GIBZE_229533 and tr_A0A2T4H8J9_A0A2T4H8J9_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A164XSS1_A0A164XSS1_9HOMO_1314777 and tr_A0A165ZYJ0_A0A165ZYJ0_9HOMO_1314776 are exactly identical!
WARNING: Duplicate sequences found: 31

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/Q8TAQ2/3_mltree/Q8TAQ2.raxml.reduced.phy

Alignment comprises 1 partitions and 503 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 503 / 503
Gaps: 11.88 %
Invariant sites: 0.40 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/3_mltree/Q8TAQ2.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 252 / 20160
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -739392.647844] Initial branch length optimization
[00:00:06 -623558.199740] Model parameter optimization (eps = 10.000000)
[00:01:16 -620489.644134] AUTODETECT spr round 1 (radius: 5)
[00:04:42 -464639.667315] AUTODETECT spr round 2 (radius: 10)
[00:08:14 -369057.176833] AUTODETECT spr round 3 (radius: 15)
[00:12:17 -304347.062922] AUTODETECT spr round 4 (radius: 20)
[00:16:44 -276324.727807] AUTODETECT spr round 5 (radius: 25)
[00:22:10 -273065.830838] SPR radius for FAST iterations: 25 (autodetect)
[00:22:10 -273065.830838] Model parameter optimization (eps = 3.000000)
[00:22:35 -272795.515568] FAST spr round 1 (radius: 25)
[00:27:21 -237048.681493] FAST spr round 2 (radius: 25)
[00:30:42 -235536.689977] FAST spr round 3 (radius: 25)
[00:33:32 -235354.228392] FAST spr round 4 (radius: 25)
[00:36:08 -235322.483194] FAST spr round 5 (radius: 25)
[00:38:26 -235311.840745] FAST spr round 6 (radius: 25)
[00:40:41 -235301.604514] FAST spr round 7 (radius: 25)
[00:42:57 -235299.138554] FAST spr round 8 (radius: 25)
[00:45:09 -235299.138482] Model parameter optimization (eps = 1.000000)
[00:45:25 -235297.396372] SLOW spr round 1 (radius: 5)
[00:48:24 -235248.684496] SLOW spr round 2 (radius: 5)
[00:51:26 -235239.347455] SLOW spr round 3 (radius: 5)
[00:54:24 -235239.332474] SLOW spr round 4 (radius: 10)
[00:57:27 -235233.121835] SLOW spr round 5 (radius: 5)
[01:01:16 -235233.086798] SLOW spr round 6 (radius: 10)
[01:04:51 -235233.086295] SLOW spr round 7 (radius: 15)
[01:09:48 -235232.660944] SLOW spr round 8 (radius: 5)
[01:13:37 -235232.659652] SLOW spr round 9 (radius: 10)
[01:17:07 -235232.659588] SLOW spr round 10 (radius: 15)
[01:22:00 -235232.659569] SLOW spr round 11 (radius: 20)
[01:30:08 -235232.659446] SLOW spr round 12 (radius: 25)
[01:40:27 -235232.440812] SLOW spr round 13 (radius: 5)
[01:44:32 -235232.440759] SLOW spr round 14 (radius: 10)
[01:48:25 -235232.440754] SLOW spr round 15 (radius: 15)
[01:50:20] [worker #2] ML tree search #3, logLikelihood: -235244.663323
[01:53:26 -235232.440749] SLOW spr round 16 (radius: 20)
[02:01:12 -235232.428327] SLOW spr round 17 (radius: 25)
[02:12:19 -235232.428322] Model parameter optimization (eps = 0.100000)

[02:12:34] [worker #0] ML tree search #1, logLikelihood: -235231.956455

[02:12:35 -741938.790209] Initial branch length optimization
[02:12:45 -625730.011590] Model parameter optimization (eps = 10.000000)
[02:13:00] [worker #1] ML tree search #2, logLikelihood: -235238.245125
[02:13:50 -622855.171036] AUTODETECT spr round 1 (radius: 5)
[02:17:23 -474173.610763] AUTODETECT spr round 2 (radius: 10)
[02:21:16 -376655.520648] AUTODETECT spr round 3 (radius: 15)
[02:25:32 -338404.587968] AUTODETECT spr round 4 (radius: 20)
[02:30:28 -310860.374368] AUTODETECT spr round 5 (radius: 25)
[02:36:04 -305988.704969] SPR radius for FAST iterations: 25 (autodetect)
[02:36:04 -305988.704969] Model parameter optimization (eps = 3.000000)
[02:36:38 -305790.237869] FAST spr round 1 (radius: 25)
[02:42:14 -238572.839880] FAST spr round 2 (radius: 25)
[02:46:01 -235537.623902] FAST spr round 3 (radius: 25)
[02:49:06 -235375.939887] FAST spr round 4 (radius: 25)
[02:51:46 -235351.584484] FAST spr round 5 (radius: 25)
[02:54:12 -235350.345951] FAST spr round 6 (radius: 25)
[02:56:34 -235350.345699] Model parameter optimization (eps = 1.000000)
[02:56:56 -235346.393221] SLOW spr round 1 (radius: 5)
[03:00:14 -235253.910415] SLOW spr round 2 (radius: 5)
[03:03:22 -235246.516114] SLOW spr round 3 (radius: 5)
[03:06:26 -235246.516036] SLOW spr round 4 (radius: 10)
[03:09:46 -235244.202962] SLOW spr round 5 (radius: 5)
[03:11:03] [worker #2] ML tree search #6, logLikelihood: -235243.274109
[03:13:42 -235244.201673] SLOW spr round 6 (radius: 10)
[03:17:19 -235244.201642] SLOW spr round 7 (radius: 15)
[03:22:37 -235243.771852] SLOW spr round 8 (radius: 5)
[03:26:49 -235243.770849] SLOW spr round 9 (radius: 10)
[03:30:39 -235243.770804] SLOW spr round 10 (radius: 15)
[03:35:56 -235243.770796] SLOW spr round 11 (radius: 20)
[03:44:35 -235243.770792] SLOW spr round 12 (radius: 25)
[03:55:55 -235243.273570] SLOW spr round 13 (radius: 5)
[04:00:15 -235243.271809] SLOW spr round 14 (radius: 10)
[04:03:37] [worker #1] ML tree search #5, logLikelihood: -235246.765752
[04:04:15 -235243.271807] SLOW spr round 15 (radius: 15)
[04:09:33 -235241.823132] SLOW spr round 16 (radius: 5)
[04:13:47 -235241.822380] SLOW spr round 17 (radius: 10)
[04:17:37 -235241.822353] SLOW spr round 18 (radius: 15)
[04:22:51 -235241.822352] SLOW spr round 19 (radius: 20)
[04:31:25 -235241.822352] SLOW spr round 20 (radius: 25)
[04:42:40 -235241.822352] Model parameter optimization (eps = 0.100000)

[04:43:00] [worker #0] ML tree search #4, logLikelihood: -235241.331820

[04:43:01 -740189.545370] Initial branch length optimization
[04:43:09 -625901.133670] Model parameter optimization (eps = 10.000000)
[04:44:18 -622986.344575] AUTODETECT spr round 1 (radius: 5)
[04:47:50 -453158.680506] AUTODETECT spr round 2 (radius: 10)
[04:51:43 -345444.496468] AUTODETECT spr round 3 (radius: 15)
[04:53:59] [worker #2] ML tree search #9, logLikelihood: -235252.175056
[04:55:57 -278483.688104] AUTODETECT spr round 4 (radius: 20)
[05:01:00 -265449.129784] AUTODETECT spr round 5 (radius: 25)
[05:06:52 -262398.036337] SPR radius for FAST iterations: 25 (autodetect)
[05:06:52 -262398.036337] Model parameter optimization (eps = 3.000000)
[05:07:19 -262139.192894] FAST spr round 1 (radius: 25)
[05:12:04 -238689.601953] FAST spr round 2 (radius: 25)
[05:15:37 -237477.315615] FAST spr round 3 (radius: 25)
[05:18:16 -236242.404763] FAST spr round 4 (radius: 25)
[05:20:46 -236036.104203] FAST spr round 5 (radius: 25)
[05:23:00 -236029.571211] FAST spr round 6 (radius: 25)
[05:25:16 -236029.571156] Model parameter optimization (eps = 1.000000)
[05:25:37 -236027.888333] SLOW spr round 1 (radius: 5)
[05:28:44 -235965.159833] SLOW spr round 2 (radius: 5)
[05:31:51 -235957.592305] SLOW spr round 3 (radius: 5)
[05:34:41 -235956.994686] SLOW spr round 4 (radius: 5)
[05:37:30 -235956.993895] SLOW spr round 5 (radius: 10)
[05:40:36 -235955.183088] SLOW spr round 6 (radius: 5)
[05:44:12 -235953.020767] SLOW spr round 7 (radius: 5)
[05:47:18 -235953.020277] SLOW spr round 8 (radius: 10)
[05:50:23 -235953.020232] SLOW spr round 9 (radius: 15)
[05:55:07 -235953.020208] SLOW spr round 10 (radius: 20)
[05:59:07] [worker #1] ML tree search #8, logLikelihood: -235254.073645
[06:02:22 -235953.020191] SLOW spr round 11 (radius: 25)
[06:12:06 -235952.411895] SLOW spr round 12 (radius: 5)
[06:16:04 -235952.410288] SLOW spr round 13 (radius: 10)
[06:19:50 -235952.409583] SLOW spr round 14 (radius: 15)
[06:24:59 -235952.409569] SLOW spr round 15 (radius: 20)
[06:32:39 -235926.901261] SLOW spr round 16 (radius: 5)
[06:36:55 -235839.802705] SLOW spr round 17 (radius: 5)
[06:39:29] [worker #2] ML tree search #12, logLikelihood: -235237.174476
[06:40:34 -235371.678523] SLOW spr round 18 (radius: 5)
[06:43:54 -235262.813588] SLOW spr round 19 (radius: 5)
[06:46:47 -235262.813240] SLOW spr round 20 (radius: 10)
[06:49:49 -235262.812369] SLOW spr round 21 (radius: 15)
[06:54:56 -235262.812119] SLOW spr round 22 (radius: 20)
[07:02:56 -235262.811883] SLOW spr round 23 (radius: 25)
[07:13:33 -235262.151015] SLOW spr round 24 (radius: 5)
[07:17:49 -235250.098839] SLOW spr round 25 (radius: 5)
[07:21:24 -235250.098646] SLOW spr round 26 (radius: 10)
[07:24:50 -235250.098469] SLOW spr round 27 (radius: 15)
[07:30:11 -235250.098311] SLOW spr round 28 (radius: 20)
[07:38:12 -235250.098300] SLOW spr round 29 (radius: 25)
[07:47:49 -235250.098299] Model parameter optimization (eps = 0.100000)

[07:47:55] [worker #0] ML tree search #7, logLikelihood: -235250.067123

[07:47:55 -738982.943431] Initial branch length optimization
[07:48:04 -625688.994835] Model parameter optimization (eps = 10.000000)
[07:49:16 -622700.481026] AUTODETECT spr round 1 (radius: 5)
[07:52:27 -460605.458276] AUTODETECT spr round 2 (radius: 10)
[07:55:53 -365766.828680] AUTODETECT spr round 3 (radius: 15)
[07:59:34 -312516.049209] AUTODETECT spr round 4 (radius: 20)
[08:03:49 -278406.968678] AUTODETECT spr round 5 (radius: 25)
[08:05:05] [worker #1] ML tree search #11, logLikelihood: -235261.414558
[08:08:41 -273125.897109] SPR radius for FAST iterations: 25 (autodetect)
[08:08:41 -273125.897109] Model parameter optimization (eps = 3.000000)
[08:09:06 -272851.336638] FAST spr round 1 (radius: 25)
[08:13:24 -237168.439726] FAST spr round 2 (radius: 25)
[08:16:26 -235508.753664] FAST spr round 3 (radius: 25)
[08:19:05 -235393.970815] FAST spr round 4 (radius: 25)
[08:21:30 -235348.817495] FAST spr round 5 (radius: 25)
[08:23:45 -235344.245638] FAST spr round 6 (radius: 25)
[08:25:56 -235342.871490] FAST spr round 7 (radius: 25)
[08:28:04 -235342.871322] Model parameter optimization (eps = 1.000000)
[08:28:22 -235340.732962] SLOW spr round 1 (radius: 5)
[08:31:12 -235256.829352] SLOW spr round 2 (radius: 5)
[08:31:20] [worker #2] ML tree search #15, logLikelihood: -235260.037131
[08:34:03 -235248.242717] SLOW spr round 3 (radius: 5)
[08:37:08 -235247.667498] SLOW spr round 4 (radius: 5)
[08:40:13 -235247.658109] SLOW spr round 5 (radius: 10)
[08:43:30 -235247.645219] SLOW spr round 6 (radius: 15)
[08:48:42 -235247.644025] SLOW spr round 7 (radius: 20)
[08:56:26 -235247.643516] SLOW spr round 8 (radius: 25)
[09:05:53 -235235.568284] SLOW spr round 9 (radius: 5)
[09:09:48 -235234.526455] SLOW spr round 10 (radius: 5)
[09:13:06 -235234.525878] SLOW spr round 11 (radius: 10)
[09:16:14 -235234.525635] SLOW spr round 12 (radius: 15)
[09:21:02 -235234.525119] SLOW spr round 13 (radius: 20)
[09:28:50] [worker #1] ML tree search #14, logLikelihood: -235239.555385
[09:29:58 -235234.524904] SLOW spr round 14 (radius: 25)
[09:42:11 -235234.524702] Model parameter optimization (eps = 0.100000)

[09:42:25] [worker #0] ML tree search #10, logLikelihood: -235234.013294

[09:42:25 -739772.338933] Initial branch length optimization
[09:42:33 -623410.421206] Model parameter optimization (eps = 10.000000)
[09:44:07 -620476.283462] AUTODETECT spr round 1 (radius: 5)
[09:48:04 -462006.921581] AUTODETECT spr round 2 (radius: 10)
[09:52:15 -364484.530085] AUTODETECT spr round 3 (radius: 15)
[09:56:54 -293110.139941] AUTODETECT spr round 4 (radius: 20)
[10:01:53 -271033.534445] AUTODETECT spr round 5 (radius: 25)
[10:07:40 -267489.095872] SPR radius for FAST iterations: 25 (autodetect)
[10:07:40 -267489.095872] Model parameter optimization (eps = 3.000000)
[10:08:07 -267286.777044] FAST spr round 1 (radius: 25)
[10:13:17 -236505.875667] FAST spr round 2 (radius: 25)
[10:17:05 -235478.589056] FAST spr round 3 (radius: 25)
[10:20:20 -235395.569802] FAST spr round 4 (radius: 25)
[10:23:14 -235386.331277] FAST spr round 5 (radius: 25)
[10:25:58 -235383.732986] FAST spr round 6 (radius: 25)
[10:28:37 -235383.732899] Model parameter optimization (eps = 1.000000)
[10:28:55 -235381.100385] SLOW spr round 1 (radius: 5)
[10:32:28 -235322.385764] SLOW spr round 2 (radius: 5)
[10:36:02 -235319.483342] SLOW spr round 3 (radius: 5)
[10:39:33 -235315.073053] SLOW spr round 4 (radius: 5)
[10:43:01 -235314.194957] SLOW spr round 5 (radius: 5)
[10:46:26 -235314.194173] SLOW spr round 6 (radius: 10)
[10:50:02 -235314.194102] SLOW spr round 7 (radius: 15)
[10:55:52 -235314.194078] SLOW spr round 8 (radius: 20)
[11:05:01 -235314.194054] SLOW spr round 9 (radius: 25)
[11:08:36] [worker #1] ML tree search #17, logLikelihood: -235257.717785
[11:17:22 -235314.193918] Model parameter optimization (eps = 0.100000)

[11:17:46] [worker #0] ML tree search #13, logLikelihood: -235313.681765

[11:17:47 -742883.635876] Initial branch length optimization
[11:17:54 -627463.880610] Model parameter optimization (eps = 10.000000)
[11:18:52 -624543.126330] AUTODETECT spr round 1 (radius: 5)
[11:22:49 -470769.213622] AUTODETECT spr round 2 (radius: 10)
[11:27:02 -367004.298079] AUTODETECT spr round 3 (radius: 15)
[11:31:48 -292130.281302] AUTODETECT spr round 4 (radius: 20)
[11:36:41 -267778.254443] AUTODETECT spr round 5 (radius: 25)
[11:43:06 -264463.637526] SPR radius for FAST iterations: 25 (autodetect)
[11:43:06 -264463.637526] Model parameter optimization (eps = 3.000000)
[11:43:38 -264272.869058] FAST spr round 1 (radius: 25)
[11:48:49 -236558.204269] FAST spr round 2 (radius: 25)
[11:52:39 -235493.267016] FAST spr round 3 (radius: 25)
[11:56:01 -235423.259981] FAST spr round 4 (radius: 25)
[11:58:53 -235414.861905] FAST spr round 5 (radius: 25)
[12:01:34 -235408.046478] FAST spr round 6 (radius: 25)
[12:04:03] [worker #2] ML tree search #18, logLikelihood: -235238.818832
[12:04:07 -235408.045591] Model parameter optimization (eps = 1.000000)
[12:04:34 -235389.802634] SLOW spr round 1 (radius: 5)
[12:08:09 -235329.303608] SLOW spr round 2 (radius: 5)
[12:11:43 -235322.713541] SLOW spr round 3 (radius: 5)
[12:15:05 -235322.712922] SLOW spr round 4 (radius: 10)
[12:18:39 -235322.712683] SLOW spr round 5 (radius: 15)
[12:24:38 -235322.712477] SLOW spr round 6 (radius: 20)
[12:33:53 -235322.646692] SLOW spr round 7 (radius: 25)
[12:46:39 -235322.512444] SLOW spr round 8 (radius: 5)
[12:51:23 -235322.511876] SLOW spr round 9 (radius: 10)
[12:51:50] [worker #1] ML tree search #20, logLikelihood: -235241.616479
[12:55:39 -235322.511735] SLOW spr round 10 (radius: 15)
[13:01:18 -235322.511622] SLOW spr round 11 (radius: 20)
[13:10:33 -235322.511059] SLOW spr round 12 (radius: 25)
[13:23:08 -235322.510900] Model parameter optimization (eps = 0.100000)

[13:23:24] [worker #0] ML tree search #16, logLikelihood: -235322.158153

[13:23:24 -742130.814073] Initial branch length optimization
[13:23:32 -625765.586318] Model parameter optimization (eps = 10.000000)
[13:24:52 -622609.097613] AUTODETECT spr round 1 (radius: 5)
[13:28:39 -462437.046438] AUTODETECT spr round 2 (radius: 10)
[13:32:47 -357791.574978] AUTODETECT spr round 3 (radius: 15)
[13:37:07 -318951.669330] AUTODETECT spr round 4 (radius: 20)
[13:42:08 -278692.851594] AUTODETECT spr round 5 (radius: 25)
[13:48:13 -269777.587063] SPR radius for FAST iterations: 25 (autodetect)
[13:48:13 -269777.587063] Model parameter optimization (eps = 3.000000)
[13:48:42 -269488.646818] FAST spr round 1 (radius: 25)
[13:53:56 -236800.712347] FAST spr round 2 (radius: 25)
[13:57:47 -235419.000960] FAST spr round 3 (radius: 25)
[14:01:07 -235375.372171] FAST spr round 4 (radius: 25)
[14:03:56 -235344.416721] FAST spr round 5 (radius: 25)
[14:06:33 -235335.831749] FAST spr round 6 (radius: 25)
[14:09:05 -235335.831603] Model parameter optimization (eps = 1.000000)
[14:09:23 -235334.731369] SLOW spr round 1 (radius: 5)
[14:12:47 -235264.596147] SLOW spr round 2 (radius: 5)
[14:16:11 -235259.473652] SLOW spr round 3 (radius: 5)
[14:19:31 -235258.987044] SLOW spr round 4 (radius: 5)
[14:22:47 -235258.986949] SLOW spr round 5 (radius: 10)
[14:26:17 -235258.986943] SLOW spr round 6 (radius: 15)
[14:32:09 -235258.428188] SLOW spr round 7 (radius: 5)
[14:36:44 -235255.629683] SLOW spr round 8 (radius: 5)
[14:40:33 -235255.628143] SLOW spr round 9 (radius: 10)
[14:44:14 -235255.628136] SLOW spr round 10 (radius: 15)
[14:49:55 -235255.628131] SLOW spr round 11 (radius: 20)
[14:59:00 -235255.628127] SLOW spr round 12 (radius: 25)
[15:10:39 -235255.576643] Model parameter optimization (eps = 0.100000)

[15:10:55] [worker #0] ML tree search #19, logLikelihood: -235255.063238


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.164269,0.363625) (0.164714,0.401903) (0.307907,0.723420) (0.363109,1.793735) 
   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: -235231.956455

AIC score: 474473.912909 / AICc score: 8518533.912909 / BIC score: 482936.196201
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=503).
         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/Q8TAQ2/3_mltree/Q8TAQ2.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/3_mltree/Q8TAQ2.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/3_mltree/Q8TAQ2.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TAQ2/3_mltree/Q8TAQ2.raxml.log

Analysis started: 05-Jul-2021 11:46:31 / finished: 06-Jul-2021 02:57:26

Elapsed time: 54655.642 seconds

Consumed energy: 4832.834 Wh (= 24 km in an electric car, or 121 km with an e-scooter!)