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 17-Jul-2021 02:44:42 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/2_msa/P56199_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199 --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/P56199/2_msa/P56199_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1396 sites

WARNING: Sequences tr_A0A1D5NUG9_A0A1D5NUG9_CHICK_9031 and sp_P32018_COEA1_CHICK_9031 are exactly identical!
WARNING: Sequences tr_A0A2I2YFM7_A0A2I2YFM7_GORGO_9595 and tr_A0A2R9CHZ0_A0A2R9CHZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PYI3_H2PYI3_PANTR_9598 and tr_A0A2R8Z7G6_A0A2R8Z7G6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QHH5_H2QHH5_PANTR_9598 and tr_A0A2R9B520_A0A2R9B520_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QQV4_H2QQV4_PANTR_9598 and tr_A0A2R9BDD7_A0A2R9BDD7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G8F2Z5_G8F2Z5_MACFA_9541 and tr_A0A2K6E677_A0A2K6E677_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5P5K0_A0A2K5P5K0_CERAT_9531 and tr_A0A2K5ZDS6_A0A2K5ZDS6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K6CB99_A0A2K6CB99_MACNE_9545 and tr_A0A2K5YVX9_A0A2K5YVX9_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 8

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/P56199/3_mltree/P56199.raxml.reduced.phy

Alignment comprises 1 partitions and 1396 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1396 / 1396
Gaps: 43.06 %
Invariant sites: 0.00 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 8 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 / 175 / 14000
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1713990.719726] Initial branch length optimization
[00:00:17 -1444823.762344] Model parameter optimization (eps = 10.000000)
[00:01:37 -1441684.875509] AUTODETECT spr round 1 (radius: 5)
[00:05:56 -930983.517233] AUTODETECT spr round 2 (radius: 10)
[00:10:58 -638672.773394] AUTODETECT spr round 3 (radius: 15)
[00:15:32 -541951.934145] AUTODETECT spr round 4 (radius: 20)
[00:20:37 -495463.548863] AUTODETECT spr round 5 (radius: 25)
[00:27:42 -474853.888223] SPR radius for FAST iterations: 25 (autodetect)
[00:27:42 -474853.888223] Model parameter optimization (eps = 3.000000)
[00:28:24 -474252.287647] FAST spr round 1 (radius: 25)
[00:34:27 -414061.611346] FAST spr round 2 (radius: 25)
[00:38:34 -411600.881573] FAST spr round 3 (radius: 25)
[00:42:32 -411463.835568] FAST spr round 4 (radius: 25)
[00:45:41 -411436.967917] FAST spr round 5 (radius: 25)
[00:48:50 -411435.899133] FAST spr round 6 (radius: 25)
[00:51:26 -411435.895902] Model parameter optimization (eps = 1.000000)
[00:51:49 -411418.648247] SLOW spr round 1 (radius: 5)
[00:56:03 -411338.790443] SLOW spr round 2 (radius: 5)
[01:00:36 -411332.396662] SLOW spr round 3 (radius: 5)
[01:04:26 -411331.459729] SLOW spr round 4 (radius: 5)
[01:08:12 -411331.458931] SLOW spr round 5 (radius: 10)
[01:12:31 -411331.458532] SLOW spr round 6 (radius: 15)
[01:20:32 -411329.573233] SLOW spr round 7 (radius: 5)
[01:26:42 -411329.573007] SLOW spr round 8 (radius: 10)
[01:31:05 -411329.572819] SLOW spr round 9 (radius: 15)
[01:36:36 -411329.572657] SLOW spr round 10 (radius: 20)
[01:46:58 -411329.572517] SLOW spr round 11 (radius: 25)
[02:00:09 -411329.572395] Model parameter optimization (eps = 0.100000)

[02:00:27] ML tree search #1, logLikelihood: -411329.223646

[02:00:27 -1734768.204180] Initial branch length optimization
[02:00:39 -1470595.964901] Model parameter optimization (eps = 10.000000)
[02:01:56 -1466846.962237] AUTODETECT spr round 1 (radius: 5)
[02:07:11 -936552.621567] AUTODETECT spr round 2 (radius: 10)
[02:10:26 -650780.296885] AUTODETECT spr round 3 (radius: 15)
[02:14:07 -526175.548623] AUTODETECT spr round 4 (radius: 20)
[02:18:09 -490141.684434] AUTODETECT spr round 5 (radius: 25)
[02:22:46 -476506.944567] SPR radius for FAST iterations: 25 (autodetect)
[02:22:46 -476506.944567] Model parameter optimization (eps = 3.000000)
[02:23:27 -475927.557040] FAST spr round 1 (radius: 25)
[02:27:43 -413721.656939] FAST spr round 2 (radius: 25)
[02:30:57 -411603.343118] FAST spr round 3 (radius: 25)
[02:33:56 -411480.965788] FAST spr round 4 (radius: 25)
[02:38:49 -411468.881018] FAST spr round 5 (radius: 25)
[02:41:06 -411466.400989] FAST spr round 6 (radius: 25)
[02:43:20 -411466.400415] Model parameter optimization (eps = 1.000000)
[02:43:42 -411457.146786] SLOW spr round 1 (radius: 5)
[02:46:54 -411364.900528] SLOW spr round 2 (radius: 5)
[02:50:05 -411351.759139] SLOW spr round 3 (radius: 5)
[02:53:08 -411343.248431] SLOW spr round 4 (radius: 5)
[02:56:26 -411337.276432] SLOW spr round 5 (radius: 5)
[02:59:20 -411337.275322] SLOW spr round 6 (radius: 10)
[03:02:19 -411336.198791] SLOW spr round 7 (radius: 5)
[03:06:01 -411336.198480] SLOW spr round 8 (radius: 10)
[03:09:32 -411336.198321] SLOW spr round 9 (radius: 15)
[03:15:02 -411334.313114] SLOW spr round 10 (radius: 5)
[03:18:58 -411334.313063] SLOW spr round 11 (radius: 10)
[03:22:42 -411334.313032] SLOW spr round 12 (radius: 15)
[03:33:01 -411334.313011] SLOW spr round 13 (radius: 20)
[03:46:06 -411334.312995] SLOW spr round 14 (radius: 25)
[04:00:35 -411334.312981] Model parameter optimization (eps = 0.100000)

[04:00:57] ML tree search #2, logLikelihood: -411332.506619

[04:00:57 -1723236.040491] Initial branch length optimization
[04:01:09 -1459391.188268] Model parameter optimization (eps = 10.000000)
[04:03:41 -1455907.383414] AUTODETECT spr round 1 (radius: 5)
[04:06:42 -944783.806728] AUTODETECT spr round 2 (radius: 10)
[04:09:57 -664432.655318] AUTODETECT spr round 3 (radius: 15)
[04:13:34 -533576.396238] AUTODETECT spr round 4 (radius: 20)
[04:17:35 -497740.882548] AUTODETECT spr round 5 (radius: 25)
[04:22:29 -475373.374377] SPR radius for FAST iterations: 25 (autodetect)
[04:22:29 -475373.374377] Model parameter optimization (eps = 3.000000)
[04:23:10 -474847.166935] FAST spr round 1 (radius: 25)
[04:27:24 -415687.084995] FAST spr round 2 (radius: 25)
[04:30:41 -411798.119845] FAST spr round 3 (radius: 25)
[04:36:37 -411461.459646] FAST spr round 4 (radius: 25)
[04:44:29 -411439.999428] FAST spr round 5 (radius: 25)
[04:46:43 -411439.987262] Model parameter optimization (eps = 1.000000)
[04:47:08 -411426.315562] SLOW spr round 1 (radius: 5)
[04:50:28 -411341.035741] SLOW spr round 2 (radius: 5)
[04:53:33 -411336.562087] SLOW spr round 3 (radius: 5)
[04:56:32 -411334.411355] SLOW spr round 4 (radius: 5)
[04:59:31 -411334.387824] SLOW spr round 5 (radius: 10)
[05:02:35 -411333.989907] SLOW spr round 6 (radius: 5)
[05:06:22 -411333.988666] SLOW spr round 7 (radius: 10)
[05:09:54 -411333.987563] SLOW spr round 8 (radius: 15)
[05:16:26 -411332.112338] SLOW spr round 9 (radius: 5)
[05:22:19 -411332.111456] SLOW spr round 10 (radius: 10)
[05:26:04 -411332.110669] SLOW spr round 11 (radius: 15)
[05:31:32 -411332.109967] SLOW spr round 12 (radius: 20)
[05:42:01 -411332.109342] SLOW spr round 13 (radius: 25)
[05:55:11 -411332.108786] Model parameter optimization (eps = 0.100000)

[05:55:24] ML tree search #3, logLikelihood: -411331.970611

[05:55:24 -1729984.998413] Initial branch length optimization
[05:55:33 -1468180.208317] Model parameter optimization (eps = 10.000000)
[05:56:38 -1464867.605095] AUTODETECT spr round 1 (radius: 5)
[05:59:43 -923807.573765] AUTODETECT spr round 2 (radius: 10)
[06:03:03 -647851.381319] AUTODETECT spr round 3 (radius: 15)
[06:06:33 -529888.457831] AUTODETECT spr round 4 (radius: 20)
[06:10:41 -479990.574008] AUTODETECT spr round 5 (radius: 25)
[06:15:27 -467004.454744] SPR radius for FAST iterations: 25 (autodetect)
[06:15:27 -467004.454744] Model parameter optimization (eps = 3.000000)
[06:16:12 -466420.585596] FAST spr round 1 (radius: 25)
[06:20:21 -413829.684905] FAST spr round 2 (radius: 25)
[06:23:37 -411589.783071] FAST spr round 3 (radius: 25)
[06:26:20 -411467.473993] FAST spr round 4 (radius: 25)
[06:28:47 -411456.921078] FAST spr round 5 (radius: 25)
[06:31:06 -411451.152662] FAST spr round 6 (radius: 25)
[06:33:21 -411451.152362] Model parameter optimization (eps = 1.000000)
[06:33:42 -411437.166287] SLOW spr round 1 (radius: 5)
[06:36:53 -411358.048297] SLOW spr round 2 (radius: 5)
[06:39:59 -411351.229176] SLOW spr round 3 (radius: 5)
[06:43:40 -411351.200303] SLOW spr round 4 (radius: 10)
[06:46:47 -411350.747292] SLOW spr round 5 (radius: 5)
[06:50:34 -411350.734122] SLOW spr round 6 (radius: 10)
[06:54:08 -411350.732629] SLOW spr round 7 (radius: 15)
[07:03:14 -411348.852442] SLOW spr round 8 (radius: 5)
[07:17:06 -411348.851235] SLOW spr round 9 (radius: 10)
[07:20:55 -411348.850152] SLOW spr round 10 (radius: 15)
[07:29:33 -411348.849181] SLOW spr round 11 (radius: 20)
[07:47:52 -411348.848311] SLOW spr round 12 (radius: 25)
[08:10:33 -411348.847532] Model parameter optimization (eps = 0.100000)

[08:10:46] ML tree search #4, logLikelihood: -411348.663663

[08:10:47 -1723826.926810] Initial branch length optimization
[08:10:55 -1456827.759328] Model parameter optimization (eps = 10.000000)
[08:12:31 -1453387.221984] AUTODETECT spr round 1 (radius: 5)
[08:15:39 -915010.983659] AUTODETECT spr round 2 (radius: 10)
[08:19:55 -659969.481468] AUTODETECT spr round 3 (radius: 15)
[08:23:26 -520892.283334] AUTODETECT spr round 4 (radius: 20)
[08:27:12 -486183.146742] AUTODETECT spr round 5 (radius: 25)
[08:33:16 -467445.239486] SPR radius for FAST iterations: 25 (autodetect)
[08:33:16 -467445.239486] Model parameter optimization (eps = 3.000000)
[08:41:32 -466902.581693] FAST spr round 1 (radius: 25)
[08:45:40 -413855.653410] FAST spr round 2 (radius: 25)
[08:48:54 -411621.692355] FAST spr round 3 (radius: 25)
[08:51:44 -411491.866489] FAST spr round 4 (radius: 25)
[08:54:09 -411482.261518] FAST spr round 5 (radius: 25)
[08:56:24 -411482.237252] Model parameter optimization (eps = 1.000000)
[08:56:48 -411457.048668] SLOW spr round 1 (radius: 5)
[09:00:07 -411361.167433] SLOW spr round 2 (radius: 5)
[09:03:16 -411349.647857] SLOW spr round 3 (radius: 5)
[09:07:57 -411348.862551] SLOW spr round 4 (radius: 5)
[09:10:55 -411348.837111] SLOW spr round 5 (radius: 10)
[09:15:59 -411348.259437] SLOW spr round 6 (radius: 5)
[09:19:46 -411348.247407] SLOW spr round 7 (radius: 10)
[09:23:16 -411348.246413] SLOW spr round 8 (radius: 15)
[09:30:57 -411346.371842] SLOW spr round 9 (radius: 5)
[09:34:51 -411346.370683] SLOW spr round 10 (radius: 10)
[09:38:32 -411346.369971] SLOW spr round 11 (radius: 15)
[09:43:52 -411346.369335] SLOW spr round 12 (radius: 20)
[09:53:49 -411346.368768] SLOW spr round 13 (radius: 25)
[10:06:29 -411346.368261] Model parameter optimization (eps = 0.100000)

[10:06:42] ML tree search #5, logLikelihood: -411345.880145

[10:06:42 -1728363.646363] Initial branch length optimization
[10:06:51 -1467459.761334] Model parameter optimization (eps = 10.000000)
[10:08:02 -1463902.691341] AUTODETECT spr round 1 (radius: 5)
[10:12:04 -927434.575270] AUTODETECT spr round 2 (radius: 10)
[10:15:18 -635347.296904] AUTODETECT spr round 3 (radius: 15)
[10:19:27 -523482.555993] AUTODETECT spr round 4 (radius: 20)
[10:24:04 -482654.412518] AUTODETECT spr round 5 (radius: 25)
[10:28:50 -468795.458609] SPR radius for FAST iterations: 25 (autodetect)
[10:28:50 -468795.458609] Model parameter optimization (eps = 3.000000)
[10:29:38 -468251.749694] FAST spr round 1 (radius: 25)
[10:34:46 -413602.717334] FAST spr round 2 (radius: 25)
[10:38:06 -411620.549893] FAST spr round 3 (radius: 25)
[10:40:59 -411510.517684] FAST spr round 4 (radius: 25)
[10:43:25 -411486.237181] FAST spr round 5 (radius: 25)
[10:45:43 -411481.872786] FAST spr round 6 (radius: 25)
[10:47:59 -411481.871982] Model parameter optimization (eps = 1.000000)
[10:48:22 -411458.313345] SLOW spr round 1 (radius: 5)
[10:51:36 -411359.530610] SLOW spr round 2 (radius: 5)
[10:54:42 -411345.790464] SLOW spr round 3 (radius: 5)
[10:57:40 -411345.788980] SLOW spr round 4 (radius: 10)
[11:00:47 -411343.738459] SLOW spr round 5 (radius: 5)
[11:04:36 -411341.710030] SLOW spr round 6 (radius: 5)
[11:07:58 -411341.709901] SLOW spr round 7 (radius: 10)
[11:11:10 -411341.709818] SLOW spr round 8 (radius: 15)
[11:16:55 -411339.829864] SLOW spr round 9 (radius: 5)
[11:20:51 -411339.829812] SLOW spr round 10 (radius: 10)
[11:24:35 -411339.829770] SLOW spr round 11 (radius: 15)
[11:30:00 -411339.829734] SLOW spr round 12 (radius: 20)
[11:40:05 -411339.829703] SLOW spr round 13 (radius: 25)
[11:52:36 -411339.829676] Model parameter optimization (eps = 0.100000)

[11:52:49] ML tree search #6, logLikelihood: -411339.583021

[11:52:49 -1725111.857786] Initial branch length optimization
[11:52:58 -1461818.020623] Model parameter optimization (eps = 10.000000)
[11:54:08 -1458368.196972] AUTODETECT spr round 1 (radius: 5)
[11:57:09 -922603.667783] AUTODETECT spr round 2 (radius: 10)
[12:00:25 -628471.002530] AUTODETECT spr round 3 (radius: 15)
[12:03:57 -494567.154889] AUTODETECT spr round 4 (radius: 20)
[12:07:50 -473980.956432] AUTODETECT spr round 5 (radius: 25)
[12:12:33 -463441.882401] SPR radius for FAST iterations: 25 (autodetect)
[12:12:33 -463441.882401] Model parameter optimization (eps = 3.000000)
[12:13:12 -462865.275635] FAST spr round 1 (radius: 25)
[12:17:18 -413727.165909] FAST spr round 2 (radius: 25)
[12:20:33 -411609.357126] FAST spr round 3 (radius: 25)
[12:23:26 -411492.160117] FAST spr round 4 (radius: 25)
[12:26:01 -411477.474790] FAST spr round 5 (radius: 25)
[12:28:16 -411476.701483] FAST spr round 6 (radius: 25)
[12:30:28 -411476.563866] FAST spr round 7 (radius: 25)
[12:32:42 -411476.563825] Model parameter optimization (eps = 1.000000)
[12:33:06 -411460.158012] SLOW spr round 1 (radius: 5)
[12:36:23 -411362.434182] SLOW spr round 2 (radius: 5)
[12:39:26 -411358.969686] SLOW spr round 3 (radius: 5)
[12:42:27 -411356.655081] SLOW spr round 4 (radius: 5)
[12:45:27 -411355.318716] SLOW spr round 5 (radius: 5)
[12:48:26 -411355.318054] SLOW spr round 6 (radius: 10)
[12:51:30 -411354.723360] SLOW spr round 7 (radius: 5)
[12:55:18 -411354.723198] SLOW spr round 8 (radius: 10)
[12:58:51 -411354.428234] SLOW spr round 9 (radius: 5)
[13:02:32 -411354.428146] SLOW spr round 10 (radius: 10)
[13:05:59 -411354.428081] SLOW spr round 11 (radius: 15)
[13:11:35 -411352.553571] SLOW spr round 12 (radius: 5)
[13:15:32 -411352.553521] SLOW spr round 13 (radius: 10)
[13:19:16 -411352.553477] SLOW spr round 14 (radius: 15)
[13:24:42 -411352.553439] SLOW spr round 15 (radius: 20)
[36:32:57 -411352.553405] SLOW spr round 16 (radius: 25)
[55:55:34 -411352.553375] Model parameter optimization (eps = 0.100000)

[55:55:50] ML tree search #7, logLikelihood: -411352.326275

[55:55:50 -1711611.803933] Initial branch length optimization
[55:55:57 -1447491.662882] Model parameter optimization (eps = 10.000000)
[55:57:03 -1444025.907009] AUTODETECT spr round 1 (radius: 5)
[56:24:27 -912576.835122] AUTODETECT spr round 2 (radius: 10)
[57:02:32 -655744.584319] AUTODETECT spr round 3 (radius: 15)
[58:13:47 -544090.469263] AUTODETECT spr round 4 (radius: 20)
[58:36:42 -476894.944532] AUTODETECT spr round 5 (radius: 25)
[58:58:10 -466717.636418] SPR radius for FAST iterations: 25 (autodetect)
[58:58:10 -466717.636418] Model parameter optimization (eps = 3.000000)
[59:02:26 -466085.199000] FAST spr round 1 (radius: 25)
[65:31:34 -414933.178062] FAST spr round 2 (radius: 25)
[73:19:26 -411690.130887] FAST spr round 3 (radius: 25)
[77:07:20 -411419.117390] FAST spr round 4 (radius: 25)
[78:43:56 -411414.666939] FAST spr round 5 (radius: 25)
[79:55:19 -411414.664668] Model parameter optimization (eps = 1.000000)
[80:01:10 -411398.493122] SLOW spr round 1 (radius: 5)
[83:02:46 -411344.280365] SLOW spr round 2 (radius: 5)
[85:41:27 -411340.709355] SLOW spr round 3 (radius: 5)
[87:45:07 -411340.706599] SLOW spr round 4 (radius: 10)
[102:30:51 -411340.332424] SLOW spr round 5 (radius: 5)
[112:10:08 -411340.331989] SLOW spr round 6 (radius: 10)
[113:36:21 -411340.331728] SLOW spr round 7 (radius: 15)
[116:14:39 -411338.461080] SLOW spr round 8 (radius: 5)
[118:33:47 -411338.460909] SLOW spr round 9 (radius: 10)
[119:37:58 -411338.460762] SLOW spr round 10 (radius: 15)
[120:37:41 -411338.460635] SLOW spr round 11 (radius: 20)
[127:31:52 -411338.460524] SLOW spr round 12 (radius: 25)
[142:20:18 -411338.460427] Model parameter optimization (eps = 0.100000)

[142:20:33] ML tree search #8, logLikelihood: -411338.439616

[142:20:33 -1719342.040173] Initial branch length optimization
[142:24:11 -1452288.242584] Model parameter optimization (eps = 10.000000)
[142:26:23 -1448812.208471] AUTODETECT spr round 1 (radius: 5)
[142:47:14 -911941.766759] AUTODETECT spr round 2 (radius: 10)
[143:16:08 -655460.497429] AUTODETECT spr round 3 (radius: 15)
[143:44:33 -558508.893332] AUTODETECT spr round 4 (radius: 20)
[144:26:38 -484407.160967] AUTODETECT spr round 5 (radius: 25)
[145:13:20 -470832.418180] SPR radius for FAST iterations: 25 (autodetect)
[145:13:20 -470832.418180] Model parameter optimization (eps = 3.000000)
[145:14:45 -470300.832781] FAST spr round 1 (radius: 25)
[146:05:06 -414184.077980] FAST spr round 2 (radius: 25)
[146:38:07 -411649.438713] FAST spr round 3 (radius: 25)
[147:04:55 -411443.484064] FAST spr round 4 (radius: 25)
[147:20:01 -411438.221958] FAST spr round 5 (radius: 25)
[147:35:51 -411438.219759] Model parameter optimization (eps = 1.000000)
[147:36:41 -411418.236180] SLOW spr round 1 (radius: 5)
[148:14:12 -411347.655438] SLOW spr round 2 (radius: 5)
[148:54:24 -411342.931791] SLOW spr round 3 (radius: 5)
[149:27:57 -411342.929461] SLOW spr round 4 (radius: 10)
[150:05:12 -411342.417705] SLOW spr round 5 (radius: 5)
[152:11:46 -411342.417145] SLOW spr round 6 (radius: 10)
[154:34:46 -411342.416856] SLOW spr round 7 (radius: 15)
[158:29:14 -411340.541835] SLOW spr round 8 (radius: 5)
[159:18:19 -411340.541751] SLOW spr round 9 (radius: 10)

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 24-Jul-2021 21:25:04 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/2_msa/P56199_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199 --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

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 1396 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1396 / 1396
Gaps: 43.06 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -411340.54, ML trees: 8, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 175 / 14000
[00:00:00] Data distribution: max. searches per worker: 12

Starting ML tree search with 20 distinct starting trees

[00:00:00 -411340.541751] SPR radius for FAST iterations: 25 (autodetect)
[00:00:00 -411340.541751] SLOW spr round 9 (radius: 10)
[00:03:43 -411340.541705] SLOW spr round 10 (radius: 15)
[00:09:00 -411340.541678] SLOW spr round 11 (radius: 20)
[00:18:37 -411340.541661] SLOW spr round 12 (radius: 25)
[00:30:47 -411340.541650] Model parameter optimization (eps = 0.100000)

[00:31:00] ML tree search #9, logLikelihood: -411340.392689

[00:31:01 -1719145.438866] Initial branch length optimization
[00:31:11 -1455141.112083] Model parameter optimization (eps = 10.000000)
[00:32:12 -1451997.436493] AUTODETECT spr round 1 (radius: 5)
[00:35:21 -933842.273704] AUTODETECT spr round 2 (radius: 10)
[00:38:45 -656152.084677] AUTODETECT spr round 3 (radius: 15)
[00:42:20 -520754.043849] AUTODETECT spr round 4 (radius: 20)
[00:46:35 -473809.301731] AUTODETECT spr round 5 (radius: 25)
[00:51:52 -466598.381850] SPR radius for FAST iterations: 25 (autodetect)
[00:51:52 -466598.381850] Model parameter optimization (eps = 3.000000)
[00:52:27 -465932.018207] FAST spr round 1 (radius: 25)
[00:56:38 -414143.048744] FAST spr round 2 (radius: 25)
[00:59:54 -411683.999734] FAST spr round 3 (radius: 25)
[01:02:39 -411496.735862] FAST spr round 4 (radius: 25)
[01:05:06 -411492.648068] FAST spr round 5 (radius: 25)
[01:07:26 -411458.972152] FAST spr round 6 (radius: 25)
[01:09:44 -411457.941491] FAST spr round 7 (radius: 25)
[01:12:01 -411457.929335] Model parameter optimization (eps = 1.000000)
[01:12:20 -411441.754787] SLOW spr round 1 (radius: 5)
[01:15:26 -411366.872897] SLOW spr round 2 (radius: 5)
[01:18:32 -411354.357051] SLOW spr round 3 (radius: 5)
[01:21:30 -411348.875424] SLOW spr round 4 (radius: 5)
[01:24:28 -411348.501195] SLOW spr round 5 (radius: 5)
[01:27:22 -411348.499588] SLOW spr round 6 (radius: 10)
[01:30:23 -411348.079841] SLOW spr round 7 (radius: 5)
[01:34:04 -411348.079226] SLOW spr round 8 (radius: 10)
[01:37:34 -411348.078844] SLOW spr round 9 (radius: 15)
[01:42:59 -411346.197179] SLOW spr round 10 (radius: 5)
[01:46:52 -411346.196890] SLOW spr round 11 (radius: 10)
[01:50:32 -411346.196636] SLOW spr round 12 (radius: 15)
[01:55:52 -411346.196411] SLOW spr round 13 (radius: 20)
[02:05:41 -411346.196211] SLOW spr round 14 (radius: 25)
[02:18:19 -411346.196034] Model parameter optimization (eps = 0.100000)

[02:18:31] ML tree search #10, logLikelihood: -411345.821145

[02:18:31 -1722014.867866] Initial branch length optimization
[02:18:42 -1453848.967389] Model parameter optimization (eps = 10.000000)
[02:20:01 -1450465.673693] AUTODETECT spr round 1 (radius: 5)
[02:23:09 -952686.918443] AUTODETECT spr round 2 (radius: 10)
[02:26:34 -657920.415558] AUTODETECT spr round 3 (radius: 15)
[02:30:12 -520406.498619] AUTODETECT spr round 4 (radius: 20)
[02:34:50 -473890.505242] AUTODETECT spr round 5 (radius: 25)
[02:39:46 -466361.866399] SPR radius for FAST iterations: 25 (autodetect)
[02:39:46 -466361.866399] Model parameter optimization (eps = 3.000000)
[02:40:25 -465808.756329] FAST spr round 1 (radius: 25)
[02:44:47 -413690.917967] FAST spr round 2 (radius: 25)
[02:48:07 -411655.668640] FAST spr round 3 (radius: 25)
[02:51:06 -411478.439549] FAST spr round 4 (radius: 25)
[02:53:36 -411468.440631] FAST spr round 5 (radius: 25)
[02:56:00 -411465.582691] FAST spr round 6 (radius: 25)
[02:58:20 -411465.582353] Model parameter optimization (eps = 1.000000)
[02:58:43 -411447.895097] SLOW spr round 1 (radius: 5)
[03:01:55 -411352.846307] SLOW spr round 2 (radius: 5)
[03:04:59 -411348.670534] SLOW spr round 3 (radius: 5)
[03:07:59 -411348.364611] SLOW spr round 4 (radius: 5)
[03:10:57 -411346.708921] SLOW spr round 5 (radius: 5)
[03:13:54 -411346.708562] SLOW spr round 6 (radius: 10)
[03:16:57 -411346.337130] SLOW spr round 7 (radius: 5)
[03:20:40 -411346.336935] SLOW spr round 8 (radius: 10)
[03:24:08 -411346.336780] SLOW spr round 9 (radius: 15)
[03:29:14 -411344.456031] SLOW spr round 10 (radius: 5)
[03:33:07 -411344.455901] SLOW spr round 11 (radius: 10)
[03:36:47 -411344.455782] SLOW spr round 12 (radius: 15)
[03:41:46 -411344.455671] SLOW spr round 13 (radius: 20)
[03:50:47 -411344.455567] SLOW spr round 14 (radius: 25)
[04:01:49 -411344.455469] Model parameter optimization (eps = 0.100000)

[04:02:07] ML tree search #11, logLikelihood: -411344.312160

[04:02:07 -1713751.607366] Initial branch length optimization
[04:02:17 -1445119.818616] Model parameter optimization (eps = 10.000000)
[04:03:39 -1441722.655000] AUTODETECT spr round 1 (radius: 5)
[04:06:51 -912623.485346] AUTODETECT spr round 2 (radius: 10)
[04:10:12 -660772.569996] AUTODETECT spr round 3 (radius: 15)
[04:14:00 -520772.112115] AUTODETECT spr round 4 (radius: 20)
[04:18:31 -470849.347988] AUTODETECT spr round 5 (radius: 25)
[04:23:13 -468180.762189] SPR radius for FAST iterations: 25 (autodetect)
[04:23:13 -468180.762189] Model parameter optimization (eps = 3.000000)
[04:24:01 -467637.879910] FAST spr round 1 (radius: 25)
[04:28:14 -414770.091209] FAST spr round 2 (radius: 25)
[04:31:45 -411657.400548] FAST spr round 3 (radius: 25)
[04:34:46 -411474.224012] FAST spr round 4 (radius: 25)
[04:37:20 -411463.854505] FAST spr round 5 (radius: 25)
[04:39:44 -411461.504365] FAST spr round 6 (radius: 25)
[04:42:04 -411461.504262] Model parameter optimization (eps = 1.000000)
[04:42:28 -411439.827724] SLOW spr round 1 (radius: 5)
[04:45:46 -411375.631962] SLOW spr round 2 (radius: 5)
[04:48:45 -411375.623496] SLOW spr round 3 (radius: 10)
[04:51:52 -411371.558447] SLOW spr round 4 (radius: 5)
[04:55:39 -411369.214376] SLOW spr round 5 (radius: 5)
[04:59:00 -411367.618822] SLOW spr round 6 (radius: 5)
[05:02:08 -411366.226820] SLOW spr round 7 (radius: 5)
[05:05:08 -411366.226576] SLOW spr round 8 (radius: 10)
[05:08:12 -411366.226433] SLOW spr round 9 (radius: 15)
[05:13:49 -411364.354662] SLOW spr round 10 (radius: 5)
[05:17:41 -411364.354518] SLOW spr round 11 (radius: 10)
[05:21:20 -411364.354385] SLOW spr round 12 (radius: 15)
[05:26:23 -411364.354260] SLOW spr round 13 (radius: 20)
[05:35:30 -411364.354142] SLOW spr round 14 (radius: 25)
[05:46:37 -411364.354030] Model parameter optimization (eps = 0.100000)

[05:46:52] ML tree search #12, logLikelihood: -411363.899686

[05:46:52 -1732893.258367] Initial branch length optimization
[05:47:01 -1461137.229726] Model parameter optimization (eps = 10.000000)
[05:48:19 -1458013.879814] AUTODETECT spr round 1 (radius: 5)
[05:51:30 -922814.585542] AUTODETECT spr round 2 (radius: 10)
[05:54:54 -626497.153623] AUTODETECT spr round 3 (radius: 15)
[05:58:37 -516096.860987] AUTODETECT spr round 4 (radius: 20)
[06:03:07 -468454.053799] AUTODETECT spr round 5 (radius: 25)
[06:08:27 -461534.417970] SPR radius for FAST iterations: 25 (autodetect)
[06:08:27 -461534.417970] Model parameter optimization (eps = 3.000000)
[06:09:22 -460960.438923] FAST spr round 1 (radius: 25)
[06:13:32 -413286.146486] FAST spr round 2 (radius: 25)
[06:16:51 -411603.689775] FAST spr round 3 (radius: 25)
[06:19:44 -411455.883435] FAST spr round 4 (radius: 25)
[06:22:13 -411449.739505] FAST spr round 5 (radius: 25)
[06:24:35 -411449.738666] Model parameter optimization (eps = 1.000000)
[06:25:06 -411441.028164] SLOW spr round 1 (radius: 5)
[06:28:20 -411345.492490] SLOW spr round 2 (radius: 5)
[06:31:25 -411335.145007] SLOW spr round 3 (radius: 5)
[06:34:24 -411335.144589] SLOW spr round 4 (radius: 10)
[06:37:29 -411334.429183] SLOW spr round 5 (radius: 5)
[06:41:12 -411334.428503] SLOW spr round 6 (radius: 10)
[06:44:41 -411334.428114] SLOW spr round 7 (radius: 15)
[06:50:02 -411332.545733] SLOW spr round 8 (radius: 5)
[06:53:55 -411332.545533] SLOW spr round 9 (radius: 10)
[06:57:36 -411332.545377] SLOW spr round 10 (radius: 15)
[07:02:53 -411332.545251] SLOW spr round 11 (radius: 20)
[07:12:38 -411332.545147] SLOW spr round 12 (radius: 25)
[07:25:08 -411332.545058] Model parameter optimization (eps = 0.100000)

[07:25:24] ML tree search #13, logLikelihood: -411332.348581

[07:25:24 -1710529.767782] Initial branch length optimization
[07:25:32 -1440670.800837] Model parameter optimization (eps = 10.000000)
[07:26:45 -1437693.136852] AUTODETECT spr round 1 (radius: 5)
[07:29:56 -926131.303832] AUTODETECT spr round 2 (radius: 10)
[07:33:16 -665514.170964] AUTODETECT spr round 3 (radius: 15)
[07:36:55 -543591.652546] AUTODETECT spr round 4 (radius: 20)
[07:41:13 -491688.954585] AUTODETECT spr round 5 (radius: 25)
[07:47:09 -471401.632640] SPR radius for FAST iterations: 25 (autodetect)
[07:47:09 -471401.632640] Model parameter optimization (eps = 3.000000)
[07:47:47 -470688.445636] FAST spr round 1 (radius: 25)
[07:52:06 -414285.155659] FAST spr round 2 (radius: 25)
[07:55:18 -411646.337954] FAST spr round 3 (radius: 25)
[07:58:11 -411480.255364] FAST spr round 4 (radius: 25)
[08:00:46 -411458.114091] FAST spr round 5 (radius: 25)
[08:03:08 -411458.113656] Model parameter optimization (eps = 1.000000)
[08:03:30 -411432.758970] SLOW spr round 1 (radius: 5)
[08:06:45 -411361.162889] SLOW spr round 2 (radius: 5)
[08:09:53 -411346.535304] SLOW spr round 3 (radius: 5)
[08:12:53 -411342.830621] SLOW spr round 4 (radius: 5)
[08:15:52 -411337.457849] SLOW spr round 5 (radius: 5)
[08:18:49 -411337.444457] SLOW spr round 6 (radius: 10)
[08:21:52 -411337.062826] SLOW spr round 7 (radius: 5)
[08:25:35 -411337.062292] SLOW spr round 8 (radius: 10)
[08:29:04 -411337.062065] SLOW spr round 9 (radius: 15)
[08:34:28 -411335.184496] SLOW spr round 10 (radius: 5)
[08:38:21 -411335.184384] SLOW spr round 11 (radius: 10)
[08:42:01 -411335.184291] SLOW spr round 12 (radius: 15)
[08:47:19 -411335.184212] SLOW spr round 13 (radius: 20)
[08:57:12 -411335.184143] SLOW spr round 14 (radius: 25)
[09:09:56 -411335.184083] Model parameter optimization (eps = 0.100000)

[09:10:10] ML tree search #14, logLikelihood: -411334.987323

[09:10:10 -1723360.659711] Initial branch length optimization
[09:10:19 -1458419.922809] Model parameter optimization (eps = 10.000000)
[09:11:33 -1454683.064499] AUTODETECT spr round 1 (radius: 5)
[09:14:43 -928650.673037] AUTODETECT spr round 2 (radius: 10)
[09:18:01 -670861.804301] AUTODETECT spr round 3 (radius: 15)
[09:21:32 -536605.303660] AUTODETECT spr round 4 (radius: 20)
[09:25:36 -470054.247265] AUTODETECT spr round 5 (radius: 25)
[09:30:53 -465509.880675] SPR radius for FAST iterations: 25 (autodetect)
[09:30:53 -465509.880675] Model parameter optimization (eps = 3.000000)
[09:31:28 -465097.420364] FAST spr round 1 (radius: 25)
[09:35:44 -414245.734675] FAST spr round 2 (radius: 25)
[09:39:06 -411626.424349] FAST spr round 3 (radius: 25)
[09:42:05 -411476.026016] FAST spr round 4 (radius: 25)
[09:44:50 -411451.014204] FAST spr round 5 (radius: 25)
[09:47:12 -411450.055967] FAST spr round 6 (radius: 25)
[09:49:30 -411450.049945] Model parameter optimization (eps = 1.000000)
[09:49:57 -411417.195228] SLOW spr round 1 (radius: 5)
[09:53:17 -411353.716596] SLOW spr round 2 (radius: 5)
[09:56:22 -411344.056146] SLOW spr round 3 (radius: 5)
[09:59:22 -411337.581185] SLOW spr round 4 (radius: 5)
[10:02:19 -411337.571951] SLOW spr round 5 (radius: 10)
[10:05:22 -411336.833583] SLOW spr round 6 (radius: 5)
[10:09:04 -411336.832603] SLOW spr round 7 (radius: 10)
[10:12:35 -411336.832054] SLOW spr round 8 (radius: 15)
[10:17:55 -411336.831678] SLOW spr round 9 (radius: 20)
[10:27:43 -411336.831394] SLOW spr round 10 (radius: 25)
[10:40:22 -411336.831169] Model parameter optimization (eps = 0.100000)

[10:40:36] ML tree search #15, logLikelihood: -411336.466068

[10:40:36 -1726481.110602] Initial branch length optimization
[10:40:44 -1458983.553618] Model parameter optimization (eps = 10.000000)
[10:41:50 -1455686.951248] AUTODETECT spr round 1 (radius: 5)
[10:45:01 -925232.470799] AUTODETECT spr round 2 (radius: 10)
[10:48:21 -650231.199506] AUTODETECT spr round 3 (radius: 15)
[10:51:56 -542324.536970] AUTODETECT spr round 4 (radius: 20)
[10:56:11 -474504.322129] AUTODETECT spr round 5 (radius: 25)
[11:01:00 -460011.157291] SPR radius for FAST iterations: 25 (autodetect)
[11:01:00 -460011.157291] Model parameter optimization (eps = 3.000000)
[11:01:38 -459464.982819] FAST spr round 1 (radius: 25)
[11:06:01 -413516.558495] FAST spr round 2 (radius: 25)
[11:09:22 -411527.128322] FAST spr round 3 (radius: 25)
[11:12:09 -411456.088857] FAST spr round 4 (radius: 25)
[11:14:37 -411454.255950] FAST spr round 5 (radius: 25)
[11:16:58 -411454.255227] Model parameter optimization (eps = 1.000000)
[11:17:18 -411447.143344] SLOW spr round 1 (radius: 5)
[11:20:32 -411354.417733] SLOW spr round 2 (radius: 5)
[11:23:35 -411349.386544] SLOW spr round 3 (radius: 5)
[11:26:34 -411348.183883] SLOW spr round 4 (radius: 5)
[11:29:31 -411348.158965] SLOW spr round 5 (radius: 10)
[11:32:36 -411346.743694] SLOW spr round 6 (radius: 5)
[11:36:21 -411344.720707] SLOW spr round 7 (radius: 5)
[11:39:40 -411344.719865] SLOW spr round 8 (radius: 10)
[11:42:53 -411344.274020] SLOW spr round 9 (radius: 5)
[11:46:34 -411344.273323] SLOW spr round 10 (radius: 10)
[11:50:02 -411344.272879] SLOW spr round 11 (radius: 15)
[11:55:33 -411342.394088] SLOW spr round 12 (radius: 5)
[11:59:26 -411342.393738] SLOW spr round 13 (radius: 10)
[12:03:09 -411342.393428] SLOW spr round 14 (radius: 15)
[12:08:32 -411342.393152] SLOW spr round 15 (radius: 20)
[12:18:28 -411342.392907] SLOW spr round 16 (radius: 25)
[12:30:53 -411342.392690] Model parameter optimization (eps = 0.100000)

[12:31:16] ML tree search #16, logLikelihood: -411341.430285

[12:31:16 -1732864.987247] Initial branch length optimization
[12:31:25 -1465768.658623] Model parameter optimization (eps = 10.000000)
[12:32:33 -1462574.578707] AUTODETECT spr round 1 (radius: 5)
[12:35:40 -926484.839257] AUTODETECT spr round 2 (radius: 10)
[12:39:00 -646695.591333] AUTODETECT spr round 3 (radius: 15)
[12:42:33 -533437.598916] AUTODETECT spr round 4 (radius: 20)
[12:46:49 -475456.684568] AUTODETECT spr round 5 (radius: 25)
[12:51:29 -470242.329746] SPR radius for FAST iterations: 25 (autodetect)
[12:51:29 -470242.329746] Model parameter optimization (eps = 3.000000)
[12:51:57 -469625.043313] FAST spr round 1 (radius: 25)
[12:56:09 -415144.391635] FAST spr round 2 (radius: 25)
[12:59:25 -411572.750246] FAST spr round 3 (radius: 25)
[13:02:16 -411454.277429] FAST spr round 4 (radius: 25)
[13:04:48 -411440.175497] FAST spr round 5 (radius: 25)
[13:07:12 -411438.750806] FAST spr round 6 (radius: 25)
[13:09:31 -411438.750793] Model parameter optimization (eps = 1.000000)
[13:10:04 -411423.381811] SLOW spr round 1 (radius: 5)
[13:13:16 -411358.370945] SLOW spr round 2 (radius: 5)
[13:16:26 -411348.608488] SLOW spr round 3 (radius: 5)
[13:19:27 -411344.491021] SLOW spr round 4 (radius: 5)
[13:22:26 -411338.668210] SLOW spr round 5 (radius: 5)
[13:25:24 -411338.667880] SLOW spr round 6 (radius: 10)
[13:28:29 -411337.181100] SLOW spr round 7 (radius: 5)
[13:32:14 -411335.161790] SLOW spr round 8 (radius: 5)
[13:35:34 -411335.161603] SLOW spr round 9 (radius: 10)
[13:38:48 -411334.742116] SLOW spr round 10 (radius: 5)
[13:42:29 -411334.741997] SLOW spr round 11 (radius: 10)
[13:45:58 -411334.741927] SLOW spr round 12 (radius: 15)
[13:51:27 -411332.866786] SLOW spr round 13 (radius: 5)
[13:55:20 -411332.866738] SLOW spr round 14 (radius: 10)
[13:59:03 -411332.866697] SLOW spr round 15 (radius: 15)
[14:04:24 -411332.866661] SLOW spr round 16 (radius: 20)
[14:14:18 -411332.866630] SLOW spr round 17 (radius: 25)
[14:26:51 -411332.866602] Model parameter optimization (eps = 0.100000)

[14:27:06] ML tree search #17, logLikelihood: -411332.739608

[14:27:06 -1730637.197820] Initial branch length optimization
[14:27:14 -1463380.577264] Model parameter optimization (eps = 10.000000)
[14:28:46 -1460287.367722] AUTODETECT spr round 1 (radius: 5)
[14:31:55 -934096.244136] AUTODETECT spr round 2 (radius: 10)
[14:35:19 -636355.323283] AUTODETECT spr round 3 (radius: 15)
[14:39:04 -513393.367152] AUTODETECT spr round 4 (radius: 20)
[14:43:46 -467207.261352] AUTODETECT spr round 5 (radius: 25)
[14:49:51 -461799.216805] SPR radius for FAST iterations: 25 (autodetect)
[14:49:51 -461799.216805] Model parameter optimization (eps = 3.000000)
[14:50:40 -461235.254945] FAST spr round 1 (radius: 25)
[14:55:08 -413247.474639] FAST spr round 2 (radius: 25)
[14:58:30 -411506.546450] FAST spr round 3 (radius: 25)
[15:01:19 -411445.167028] FAST spr round 4 (radius: 25)
[15:03:52 -411435.718297] FAST spr round 5 (radius: 25)
[15:06:14 -411433.059991] FAST spr round 6 (radius: 25)
[15:08:33 -411433.059937] Model parameter optimization (eps = 1.000000)
[15:09:03 -411419.958982] SLOW spr round 1 (radius: 5)
[15:12:14 -411359.853139] SLOW spr round 2 (radius: 5)
[15:15:21 -411347.642371] SLOW spr round 3 (radius: 5)
[15:18:20 -411341.761089] SLOW spr round 4 (radius: 5)
[15:21:16 -411341.740832] SLOW spr round 5 (radius: 10)
[15:24:20 -411341.320628] SLOW spr round 6 (radius: 5)
[15:28:04 -411341.320063] SLOW spr round 7 (radius: 10)
[15:31:34 -411341.319709] SLOW spr round 8 (radius: 15)
[15:37:01 -411339.434505] SLOW spr round 9 (radius: 5)
[15:40:53 -411339.434228] SLOW spr round 10 (radius: 10)
[15:44:36 -411339.433983] SLOW spr round 11 (radius: 15)
[15:49:57 -411339.433766] SLOW spr round 12 (radius: 20)
[16:00:01 -411339.433574] SLOW spr round 13 (radius: 25)
[16:12:51 -411339.433404] Model parameter optimization (eps = 0.100000)

[16:12:57] ML tree search #18, logLikelihood: -411339.396359

[16:12:57 -1731401.657807] Initial branch length optimization
[16:13:06 -1468219.500325] Model parameter optimization (eps = 10.000000)
[16:14:31 -1464753.536441] AUTODETECT spr round 1 (radius: 5)
[16:17:43 -918694.235051] AUTODETECT spr round 2 (radius: 10)
[16:21:04 -667930.245297] AUTODETECT spr round 3 (radius: 15)
[16:24:51 -532588.545768] AUTODETECT spr round 4 (radius: 20)
[16:29:29 -481591.168398] AUTODETECT spr round 5 (radius: 25)
[16:34:26 -474329.814692] SPR radius for FAST iterations: 25 (autodetect)
[16:34:26 -474329.814692] Model parameter optimization (eps = 3.000000)
[16:35:07 -473877.384288] FAST spr round 1 (radius: 25)
[16:39:18 -414501.375451] FAST spr round 2 (radius: 25)
[16:42:37 -411759.922172] FAST spr round 3 (radius: 25)
[16:45:33 -411474.996191] FAST spr round 4 (radius: 25)
[16:48:06 -411454.175924] FAST spr round 5 (radius: 25)
[16:50:27 -411454.160839] Model parameter optimization (eps = 1.000000)
[16:50:48 -411433.105831] SLOW spr round 1 (radius: 5)
[16:54:09 -411359.322460] SLOW spr round 2 (radius: 5)
[16:57:16 -411353.856487] SLOW spr round 3 (radius: 5)
[17:00:18 -411351.349809] SLOW spr round 4 (radius: 5)
[17:03:15 -411351.349583] SLOW spr round 5 (radius: 10)
[17:06:18 -411350.967672] SLOW spr round 6 (radius: 5)
[17:10:02 -411350.967640] SLOW spr round 7 (radius: 10)
[17:13:30 -411350.967634] SLOW spr round 8 (radius: 15)
[17:18:47 -411348.860616] SLOW spr round 9 (radius: 5)
[17:22:39 -411348.860611] SLOW spr round 10 (radius: 10)
[17:26:20 -411348.860610] SLOW spr round 11 (radius: 15)
[17:31:30 -411348.860609] SLOW spr round 12 (radius: 20)
[17:40:57 -411348.860608] SLOW spr round 13 (radius: 25)
[17:53:07 -411348.860607] Model parameter optimization (eps = 0.100000)

[17:53:17] ML tree search #19, logLikelihood: -411348.775180

[17:53:18 -1717405.885895] Initial branch length optimization
[17:53:27 -1453093.783990] Model parameter optimization (eps = 10.000000)
[17:54:38 -1450071.598074] AUTODETECT spr round 1 (radius: 5)
[17:57:47 -911814.161643] AUTODETECT spr round 2 (radius: 10)
[18:01:06 -650251.018619] AUTODETECT spr round 3 (radius: 15)
[18:04:45 -512713.977530] AUTODETECT spr round 4 (radius: 20)
[18:08:49 -470456.549396] AUTODETECT spr round 5 (radius: 25)
[18:13:26 -460010.166460] SPR radius for FAST iterations: 25 (autodetect)
[18:13:26 -460010.166460] Model parameter optimization (eps = 3.000000)
[18:14:10 -459333.347100] FAST spr round 1 (radius: 25)
[18:18:35 -413328.226151] FAST spr round 2 (radius: 25)
[18:21:56 -411571.453533] FAST spr round 3 (radius: 25)
[18:24:47 -411477.024070] FAST spr round 4 (radius: 25)
[18:27:22 -411470.754113] FAST spr round 5 (radius: 25)
[18:29:44 -411470.753956] Model parameter optimization (eps = 1.000000)
[18:30:13 -411457.874503] SLOW spr round 1 (radius: 5)
[18:33:27 -411370.421033] SLOW spr round 2 (radius: 5)
[18:36:32 -411366.727126] SLOW spr round 3 (radius: 5)
[18:39:33 -411364.612287] SLOW spr round 4 (radius: 5)
[18:42:32 -411360.847041] SLOW spr round 5 (radius: 5)
[18:45:34 -411357.030195] SLOW spr round 6 (radius: 5)
[18:48:32 -411355.898127] SLOW spr round 7 (radius: 5)
[18:51:32 -411348.796074] SLOW spr round 8 (radius: 5)
[18:54:29 -411348.795224] SLOW spr round 9 (radius: 10)
[18:57:32 -411348.795085] SLOW spr round 10 (radius: 15)
[19:03:21 -411346.690370] SLOW spr round 11 (radius: 5)
[19:07:14 -411346.690278] SLOW spr round 12 (radius: 10)
[19:10:54 -411346.690201] SLOW spr round 13 (radius: 15)
[19:16:06 -411346.690134] SLOW spr round 14 (radius: 20)
[19:25:44 -411346.690076] SLOW spr round 15 (radius: 25)
[19:38:05 -411346.690025] Model parameter optimization (eps = 0.100000)

[19:38:27] ML tree search #20, logLikelihood: -411346.088916


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.140365,0.494963) (0.112822,0.503480) (0.415488,0.806838) (0.331326,1.625259) 
   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: -411329.223646

AIC score: 826668.447292 / AICc score: 8870728.447292 / BIC score: 837177.386690
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1396).
         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/P56199/3_mltree/P56199.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P56199/3_mltree/P56199.raxml.log

Analysis started: 24-Jul-2021 21:25:04 / finished: 25-Jul-2021 17:03:32

Elapsed time: 70707.462 seconds (this run) / 644206.467 seconds (total with restarts)