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 08-Jul-2021 19:04:11 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/2_msa/P18564_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564 --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/P18564/2_msa/P18564_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 761 sites

WARNING: Sequences tr_A0A2I2YIM6_A0A2I2YIM6_GORGO_9595 and tr_A0A2R9BT83_A0A2R9BT83_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SCU5_A0A2I3SCU5_PANTR_9598 and tr_A0A2R9BLH6_A0A2R9BLH6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QZT0_A0A1D5QZT0_MACMU_9544 and tr_A0A2K5MWS1_A0A2K5MWS1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7BW06_F7BW06_MACMU_9544 and tr_A0A2K6BHY6_A0A2K6BHY6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7F3K9_F7F3K9_MACMU_9544 and tr_G7P0S0_G7P0S0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FG54_F7FG54_MACMU_9544 and tr_G7PV32_G7PV32_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FG54_F7FG54_MACMU_9544 and tr_A0A2I3MIT0_A0A2I3MIT0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7FG54_F7FG54_MACMU_9544 and tr_A0A2K5LTD1_A0A2K5LTD1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FG54_F7FG54_MACMU_9544 and tr_A0A2K6BAZ5_A0A2K6BAZ5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FG54_F7FG54_MACMU_9544 and tr_A0A2K5YHH7_A0A2K5YHH7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7GE04_F7GE04_MACMU_9544 and tr_A0A2K6DXI5_A0A2K6DXI5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_E5SPE4_E5SPE4_TRISP_6334 and tr_A0A0V0RZ31_A0A0V0RZ31_9BILA_6336 are exactly identical!
WARNING: Sequences tr_E5SPE4_E5SPE4_TRISP_6334 and tr_A0A0V0ZRE4_A0A0V0ZRE4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_H0YRV7_H0YRV7_TAEGU_59729 and tr_A0A218V6Y2_A0A218V6Y2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A8WVF5_A8WVF5_CAEBR_6238 and tr_A0A2G5UJ11_A0A2G5UJ11_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A0A096MY76_A0A096MY76_PAPAN_9555 and tr_A0A2K5MNH6_A0A2K5MNH6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MB35_A0A2I3MB35_PAPAN_9555 and tr_A0A2K6AYZ7_A0A2K6AYZ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0V1CWA6_A0A0V1CWA6_TRIBR_45882 and tr_A0A0V1LAI2_A0A0V1LAI2_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CWA6_A0A0V1CWA6_TRIBR_45882 and tr_A0A0V1PDF2_A0A0V1PDF2_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0V9F0_A0A0V0V9F0_9BILA_181606 and tr_A0A0V0TWR6_A0A0V0TWR6_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2I4AII0_A0A2I4AII0_9TELE_52670 and tr_A0A2I4D3T8_A0A2I4D3T8_9TELE_52670 are exactly identical!
WARNING: Duplicate sequences found: 21

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/P18564/3_mltree/P18564.raxml.reduced.phy

Alignment comprises 1 partitions and 761 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 761 / 761
Gaps: 7.63 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 191 / 15280
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1328730.807411] Initial branch length optimization
[00:00:10 -1134834.945120] Model parameter optimization (eps = 10.000000)
[00:00:57 -1134346.953289] AUTODETECT spr round 1 (radius: 5)
[00:04:32 -746822.200266] AUTODETECT spr round 2 (radius: 10)
[00:08:23 -551684.097309] AUTODETECT spr round 3 (radius: 15)
[00:12:46 -434356.876587] AUTODETECT spr round 4 (radius: 20)
[00:17:19 -403057.808091] AUTODETECT spr round 5 (radius: 25)
[00:22:19 -399636.789762] SPR radius for FAST iterations: 25 (autodetect)
[00:22:19 -399636.789762] Model parameter optimization (eps = 3.000000)
[00:22:44 -399425.728831] FAST spr round 1 (radius: 25)
[00:27:05 -354262.017925] FAST spr round 2 (radius: 25)
[00:30:19 -352827.339478] FAST spr round 3 (radius: 25)
[00:33:08 -352722.262730] FAST spr round 4 (radius: 25)
[00:35:31 -352706.420023] FAST spr round 5 (radius: 25)
[00:37:45 -352706.341527] Model parameter optimization (eps = 1.000000)
[00:38:00 -352703.094541] SLOW spr round 1 (radius: 5)
[00:41:10 -352645.403001] SLOW spr round 2 (radius: 5)
[00:44:19 -352638.659295] SLOW spr round 3 (radius: 5)
[00:47:19 -352638.658206] SLOW spr round 4 (radius: 10)
[00:50:21 -352638.657317] SLOW spr round 5 (radius: 15)
[00:55:41 -352638.656423] SLOW spr round 6 (radius: 20)
[01:04:46 -352637.891299] SLOW spr round 7 (radius: 5)
[01:08:41 -352634.905738] SLOW spr round 8 (radius: 5)
[01:12:03 -352634.905738] SLOW spr round 9 (radius: 10)
[01:15:07 -352634.905738] SLOW spr round 10 (radius: 15)
[01:20:04 -352634.905738] SLOW spr round 11 (radius: 20)
[01:29:13 -352634.905737] SLOW spr round 12 (radius: 25)
[01:30:15] [worker #1] ML tree search #2, logLikelihood: -352593.071142
[01:41:47 -352634.905737] Model parameter optimization (eps = 0.100000)

[01:42:05] [worker #0] ML tree search #1, logLikelihood: -352634.736175

[01:42:05 -1323323.021256] Initial branch length optimization
[01:42:14 -1131992.322345] Model parameter optimization (eps = 10.000000)
[01:42:56 -1131638.063472] AUTODETECT spr round 1 (radius: 5)
[01:46:25 -748440.503038] AUTODETECT spr round 2 (radius: 10)
[01:50:15 -562249.297626] AUTODETECT spr round 3 (radius: 15)
[01:54:25 -501366.639903] AUTODETECT spr round 4 (radius: 20)
[01:59:24 -442144.688574] AUTODETECT spr round 5 (radius: 25)
[02:05:56 -426847.871297] SPR radius for FAST iterations: 25 (autodetect)
[02:05:56 -426847.871297] Model parameter optimization (eps = 3.000000)
[02:06:24 -426684.561008] FAST spr round 1 (radius: 25)
[02:10:48 -356232.341893] FAST spr round 2 (radius: 25)
[02:14:05 -352974.762598] FAST spr round 3 (radius: 25)
[02:16:51 -352774.304512] FAST spr round 4 (radius: 25)
[02:19:20 -352752.895782] FAST spr round 5 (radius: 25)
[02:21:40 -352747.526004] FAST spr round 6 (radius: 25)
[02:23:58 -352747.526001] Model parameter optimization (eps = 1.000000)
[02:24:05 -352746.556893] SLOW spr round 1 (radius: 5)
[02:27:27 -352653.459097] SLOW spr round 2 (radius: 5)
[02:30:34 -352640.773295] SLOW spr round 3 (radius: 5)
[02:33:32 -352634.505490] SLOW spr round 4 (radius: 5)
[02:36:29 -352632.652926] SLOW spr round 5 (radius: 5)
[02:39:25 -352632.087061] SLOW spr round 6 (radius: 5)
[02:42:20 -352632.086694] SLOW spr round 7 (radius: 10)
[02:45:22 -352631.784015] SLOW spr round 8 (radius: 5)
[02:49:05 -352628.644433] SLOW spr round 9 (radius: 5)
[02:52:18 -352628.644348] SLOW spr round 10 (radius: 10)
[02:55:19 -352628.644291] SLOW spr round 11 (radius: 15)
[03:00:28 -352628.644248] SLOW spr round 12 (radius: 20)
[03:09:44 -352628.644215] SLOW spr round 13 (radius: 25)
[03:12:39] [worker #1] ML tree search #4, logLikelihood: -352595.611601
[03:22:40 -352628.644190] Model parameter optimization (eps = 0.100000)

[03:23:03] [worker #0] ML tree search #3, logLikelihood: -352607.900720

[03:23:03 -1322030.230278] Initial branch length optimization
[03:23:13 -1130256.730336] Model parameter optimization (eps = 10.000000)
[03:24:09 -1129820.403791] AUTODETECT spr round 1 (radius: 5)
[03:27:40 -737988.980965] AUTODETECT spr round 2 (radius: 10)
[03:31:25 -562359.682841] AUTODETECT spr round 3 (radius: 15)
[03:35:37 -457589.421318] AUTODETECT spr round 4 (radius: 20)
[03:42:48 -413208.850559] AUTODETECT spr round 5 (radius: 25)
[03:49:22 -400197.628816] SPR radius for FAST iterations: 25 (autodetect)
[03:49:22 -400197.628816] Model parameter optimization (eps = 3.000000)
[03:49:48 -399999.789320] FAST spr round 1 (radius: 25)
[03:54:08 -354832.218445] FAST spr round 2 (radius: 25)
[03:57:20 -352882.132718] FAST spr round 3 (radius: 25)
[04:00:11 -352702.465103] FAST spr round 4 (radius: 25)
[04:02:37 -352694.964690] FAST spr round 5 (radius: 25)
[04:04:56 -352694.953478] Model parameter optimization (eps = 1.000000)
[04:05:14 -352693.330356] SLOW spr round 1 (radius: 5)
[04:08:35 -352636.594829] SLOW spr round 2 (radius: 5)
[04:11:41 -352630.393230] SLOW spr round 3 (radius: 5)
[04:14:41 -352629.420397] SLOW spr round 4 (radius: 5)
[04:17:35 -352629.419931] SLOW spr round 5 (radius: 10)
[04:20:33 -352629.419930] SLOW spr round 6 (radius: 15)
[04:25:54 -352629.419930] SLOW spr round 7 (radius: 20)
[04:34:53 -352629.419930] SLOW spr round 8 (radius: 25)
[04:47:44 -352629.419930] Model parameter optimization (eps = 0.100000)

[04:47:54] [worker #0] ML tree search #5, logLikelihood: -352629.379714

[04:47:54 -1314493.006161] Initial branch length optimization
[04:48:03 -1126199.433082] Model parameter optimization (eps = 10.000000)
[04:48:58 -1125768.043616] AUTODETECT spr round 1 (radius: 5)
[04:52:27 -756862.087902] AUTODETECT spr round 2 (radius: 10)
[04:56:21 -555438.297024] AUTODETECT spr round 3 (radius: 15)
[04:59:51] [worker #1] ML tree search #6, logLikelihood: -352608.118686
[05:00:35 -459193.191306] AUTODETECT spr round 4 (radius: 20)
[05:05:57 -420041.361430] AUTODETECT spr round 5 (radius: 25)
[05:10:51 -397965.078079] SPR radius for FAST iterations: 25 (autodetect)
[05:10:51 -397965.078079] Model parameter optimization (eps = 3.000000)
[05:11:17 -397770.933968] FAST spr round 1 (radius: 25)
[05:15:28 -354912.590748] FAST spr round 2 (radius: 25)
[05:18:36 -352987.017919] FAST spr round 3 (radius: 25)
[05:21:21 -352766.434726] FAST spr round 4 (radius: 25)
[05:23:49 -352730.751031] FAST spr round 5 (radius: 25)
[05:26:14 -352723.186012] FAST spr round 6 (radius: 25)
[05:28:33 -352720.814247] FAST spr round 7 (radius: 25)
[05:30:52 -352720.813434] Model parameter optimization (eps = 1.000000)
[05:31:10 -352717.323589] SLOW spr round 1 (radius: 5)
[05:34:27 -352613.330671] SLOW spr round 2 (radius: 5)
[05:37:36 -352597.781439] SLOW spr round 3 (radius: 5)
[05:40:38 -352595.650961] SLOW spr round 4 (radius: 5)
[05:43:39 -352595.650246] SLOW spr round 5 (radius: 10)
[05:46:41 -352595.649535] SLOW spr round 6 (radius: 15)
[05:51:54 -352595.648818] SLOW spr round 7 (radius: 20)
[06:00:51 -352595.648095] SLOW spr round 8 (radius: 25)
[06:13:41 -352595.647366] Model parameter optimization (eps = 0.100000)

[06:13:48] [worker #0] ML tree search #7, logLikelihood: -352595.567970

[06:13:48 -1319312.705214] Initial branch length optimization
[06:13:56 -1127708.494459] Model parameter optimization (eps = 10.000000)
[06:14:43 -1127320.381637] AUTODETECT spr round 1 (radius: 5)
[06:18:19 -754563.247248] AUTODETECT spr round 2 (radius: 10)
[06:22:14 -554368.326111] AUTODETECT spr round 3 (radius: 15)
[06:26:22 -450835.901553] AUTODETECT spr round 4 (radius: 20)
[06:33:14 -414129.866512] AUTODETECT spr round 5 (radius: 25)
[06:39:13 -403443.040509] SPR radius for FAST iterations: 25 (autodetect)
[06:39:13 -403443.040509] Model parameter optimization (eps = 3.000000)
[06:39:39 -403232.153263] FAST spr round 1 (radius: 25)
[06:44:01 -354543.146501] FAST spr round 2 (radius: 25)
[06:47:02] [worker #1] ML tree search #8, logLikelihood: -352586.714186
[06:47:10 -352792.542914] FAST spr round 3 (radius: 25)
[06:49:55 -352730.139252] FAST spr round 4 (radius: 25)
[06:52:21 -352728.047331] FAST spr round 5 (radius: 25)
[06:54:42 -352728.046671] Model parameter optimization (eps = 1.000000)
[06:55:01 -352723.091733] SLOW spr round 1 (radius: 5)
[06:58:26 -352607.633491] SLOW spr round 2 (radius: 5)
[07:01:37 -352602.459491] SLOW spr round 3 (radius: 5)
[07:04:41 -352598.775694] SLOW spr round 4 (radius: 5)
[07:07:40 -352598.775024] SLOW spr round 5 (radius: 10)
[07:10:42 -352598.774395] SLOW spr round 6 (radius: 15)
[07:16:03 -352598.754210] SLOW spr round 7 (radius: 20)
[07:24:46 -352598.753566] SLOW spr round 8 (radius: 25)
[07:37:22 -352598.752918] Model parameter optimization (eps = 0.100000)

[07:37:37] [worker #0] ML tree search #9, logLikelihood: -352597.949918

[07:37:37 -1323170.839402] Initial branch length optimization
[07:37:45 -1130296.381502] Model parameter optimization (eps = 10.000000)
[07:38:38 -1129857.411497] AUTODETECT spr round 1 (radius: 5)
[07:42:11 -748281.763292] AUTODETECT spr round 2 (radius: 10)
[07:46:05 -541363.831572] AUTODETECT spr round 3 (radius: 15)
[07:50:24 -434402.967364] AUTODETECT spr round 4 (radius: 20)
[07:56:32 -410748.961711] AUTODETECT spr round 5 (radius: 25)
[08:01:51 -404312.444761] SPR radius for FAST iterations: 25 (autodetect)
[08:01:51 -404312.444761] Model parameter optimization (eps = 3.000000)
[08:02:00 -404309.833777] FAST spr round 1 (radius: 25)
[08:06:00 -357715.024632] FAST spr round 2 (radius: 25)
[08:09:02 -353209.178716] FAST spr round 3 (radius: 25)
[08:11:44 -352928.843173] FAST spr round 4 (radius: 25)
[08:14:08 -352915.665462] FAST spr round 5 (radius: 25)
[08:16:26 -352914.960657] FAST spr round 6 (radius: 25)
[08:17:43] [worker #1] ML tree search #10, logLikelihood: -352624.152659
[08:18:44 -352914.960510] Model parameter optimization (eps = 1.000000)
[08:19:03 -352738.342942] SLOW spr round 1 (radius: 5)
[08:22:25 -352638.437951] SLOW spr round 2 (radius: 5)
[08:25:38 -352635.727296] SLOW spr round 3 (radius: 5)
[08:28:44 -352635.271354] SLOW spr round 4 (radius: 5)
[08:31:45 -352635.271341] SLOW spr round 5 (radius: 10)
[08:34:50 -352632.840866] SLOW spr round 6 (radius: 5)
[08:38:37 -352631.202386] SLOW spr round 7 (radius: 5)
[08:41:59 -352623.801442] SLOW spr round 8 (radius: 5)
[08:45:04 -352623.801308] SLOW spr round 9 (radius: 10)
[08:48:06 -352623.801301] SLOW spr round 10 (radius: 15)
[08:53:26 -352623.801294] SLOW spr round 11 (radius: 20)
[09:02:26 -352622.988102] SLOW spr round 12 (radius: 5)
[09:06:29 -352620.029410] SLOW spr round 13 (radius: 5)
[09:10:03 -352620.029403] SLOW spr round 14 (radius: 10)
[09:13:20 -352620.029396] SLOW spr round 15 (radius: 15)
[09:18:23 -352620.029389] SLOW spr round 16 (radius: 20)
[09:27:27 -352620.029382] SLOW spr round 17 (radius: 25)
[09:39:33 -352620.029375] Model parameter optimization (eps = 0.100000)

[09:39:52] [worker #0] ML tree search #11, logLikelihood: -352617.130412

[09:39:52 -1318353.562252] Initial branch length optimization
[09:40:01 -1127422.349053] Model parameter optimization (eps = 10.000000)
[09:40:49 -1127097.000435] AUTODETECT spr round 1 (radius: 5)
[09:44:17 -759066.842625] AUTODETECT spr round 2 (radius: 10)
[09:48:09 -559755.402464] AUTODETECT spr round 3 (radius: 15)
[09:50:44] [worker #1] ML tree search #12, logLikelihood: -352616.431922
[09:52:31 -482198.999858] AUTODETECT spr round 4 (radius: 20)
[09:58:28 -422613.702370] AUTODETECT spr round 5 (radius: 25)
[10:03:56 -410243.517525] SPR radius for FAST iterations: 25 (autodetect)
[10:03:56 -410243.517525] Model parameter optimization (eps = 3.000000)
[10:04:23 -410023.617077] FAST spr round 1 (radius: 25)
[10:08:29 -356493.881812] FAST spr round 2 (radius: 25)
[10:11:35 -352951.281289] FAST spr round 3 (radius: 25)
[10:14:13 -352729.457533] FAST spr round 4 (radius: 25)
[10:16:33 -352724.198849] FAST spr round 5 (radius: 25)
[10:18:48 -352723.325854] FAST spr round 6 (radius: 25)
[10:21:01 -352723.325773] Model parameter optimization (eps = 1.000000)
[10:21:31 -352706.868747] SLOW spr round 1 (radius: 5)
[10:24:52 -352633.346087] SLOW spr round 2 (radius: 5)
[10:27:58 -352630.696967] SLOW spr round 3 (radius: 5)
[10:30:56 -352630.696826] SLOW spr round 4 (radius: 10)
[10:33:56 -352630.696824] SLOW spr round 5 (radius: 15)
[10:39:19 -352630.478661] SLOW spr round 6 (radius: 5)
[10:43:09 -352630.478661] SLOW spr round 7 (radius: 10)
[10:46:44 -352630.478661] SLOW spr round 8 (radius: 15)
[10:51:35 -352630.478661] SLOW spr round 9 (radius: 20)
[11:01:02 -352630.478661] SLOW spr round 10 (radius: 25)
[11:13:22 -352630.478661] Model parameter optimization (eps = 0.100000)
[11:13:33] [worker #1] ML tree search #14, logLikelihood: -352609.540159

[11:13:35] [worker #0] ML tree search #13, logLikelihood: -352630.243471

[11:13:36 -1324753.498165] Initial branch length optimization
[11:13:45 -1134081.294481] Model parameter optimization (eps = 10.000000)
[11:14:51 -1133694.416377] AUTODETECT spr round 1 (radius: 5)
[11:18:21 -755774.219688] AUTODETECT spr round 2 (radius: 10)
[11:22:08 -538046.322904] AUTODETECT spr round 3 (radius: 15)
[11:26:12 -462059.620701] AUTODETECT spr round 4 (radius: 20)
[11:32:59 -417384.948186] AUTODETECT spr round 5 (radius: 25)
[11:39:03 -405910.078537] SPR radius for FAST iterations: 25 (autodetect)
[11:39:03 -405910.078537] Model parameter optimization (eps = 3.000000)
[11:39:26 -405754.519672] FAST spr round 1 (radius: 25)
[11:43:29 -354587.108737] FAST spr round 2 (radius: 25)
[11:46:35 -352815.277534] FAST spr round 3 (radius: 25)
[11:49:10 -352752.062037] FAST spr round 4 (radius: 25)
[11:51:30 -352738.858006] FAST spr round 5 (radius: 25)
[11:53:41 -352738.846911] Model parameter optimization (eps = 1.000000)
[11:53:58 -352732.096257] SLOW spr round 1 (radius: 5)
[11:57:06 -352630.148980] SLOW spr round 2 (radius: 5)
[12:00:08 -352617.881627] SLOW spr round 3 (radius: 5)
[12:03:04 -352617.881045] SLOW spr round 4 (radius: 10)
[12:06:01 -352609.269649] SLOW spr round 5 (radius: 5)
[12:09:38 -352605.205050] SLOW spr round 6 (radius: 5)
[12:12:47 -352605.204728] SLOW spr round 7 (radius: 10)
[12:15:48 -352605.204548] SLOW spr round 8 (radius: 15)
[12:20:52 -352604.298775] SLOW spr round 9 (radius: 5)
[12:24:39 -352601.385583] SLOW spr round 10 (radius: 5)
[12:27:56 -352601.385167] SLOW spr round 11 (radius: 10)
[12:31:00 -352601.385097] SLOW spr round 12 (radius: 15)
[12:33:05] [worker #1] ML tree search #16, logLikelihood: -352600.339744
[12:36:02 -352601.385038] SLOW spr round 13 (radius: 20)
[12:45:05 -352601.384990] SLOW spr round 14 (radius: 25)
[12:57:24 -352601.384949] Model parameter optimization (eps = 0.100000)

[12:57:39] [worker #0] ML tree search #15, logLikelihood: -352600.814659

[12:57:39 -1323095.276879] Initial branch length optimization
[12:57:50 -1132279.687950] Model parameter optimization (eps = 10.000000)
[12:58:45 -1131850.418503] AUTODETECT spr round 1 (radius: 5)
[13:02:16 -741973.249371] AUTODETECT spr round 2 (radius: 10)
[13:05:58 -531853.479708] AUTODETECT spr round 3 (radius: 15)
[13:09:55 -446364.851544] AUTODETECT spr round 4 (radius: 20)
[13:16:04 -423937.657256] AUTODETECT spr round 5 (radius: 25)
[13:22:01 -408345.216266] SPR radius for FAST iterations: 25 (autodetect)
[13:22:01 -408345.216266] Model parameter optimization (eps = 3.000000)
[13:22:26 -408153.772454] FAST spr round 1 (radius: 25)
[13:26:30 -355522.961777] FAST spr round 2 (radius: 25)
[13:29:33 -352876.792225] FAST spr round 3 (radius: 25)
[13:32:16 -352731.611432] FAST spr round 4 (radius: 25)
[13:34:40 -352706.382627] FAST spr round 5 (radius: 25)
[13:36:51 -352706.382617] Model parameter optimization (eps = 1.000000)
[13:37:12 -352696.762368] SLOW spr round 1 (radius: 5)
[13:40:29 -352605.443690] SLOW spr round 2 (radius: 5)
[13:43:36 -352591.098863] SLOW spr round 3 (radius: 5)
[13:46:41 -352583.371835] SLOW spr round 4 (radius: 5)
[13:49:32 -352583.371115] SLOW spr round 5 (radius: 10)
[13:52:28 -352583.371110] SLOW spr round 6 (radius: 15)
[13:57:50 -352583.160844] SLOW spr round 7 (radius: 5)
[14:01:37 -352583.160844] SLOW spr round 8 (radius: 10)
[14:05:12 -352583.160844] SLOW spr round 9 (radius: 15)
[14:10:04 -352583.160843] SLOW spr round 10 (radius: 20)
[14:19:33 -352583.160843] SLOW spr round 11 (radius: 25)
[14:31:40 -352583.160843] Model parameter optimization (eps = 0.100000)

[14:31:47] [worker #0] ML tree search #17, logLikelihood: -352583.123076

[14:31:47 -1322443.488128] Initial branch length optimization
[14:31:57 -1131242.164591] Model parameter optimization (eps = 10.000000)
[14:32:48 -1130700.233634] AUTODETECT spr round 1 (radius: 5)
[14:35:10] [worker #1] ML tree search #18, logLikelihood: -352629.505744
[14:36:17 -750847.925888] AUTODETECT spr round 2 (radius: 10)
[14:40:05 -527325.243933] AUTODETECT spr round 3 (radius: 15)
[14:44:19 -438877.453717] AUTODETECT spr round 4 (radius: 20)
[14:49:16 -396597.698164] AUTODETECT spr round 5 (radius: 25)
[14:54:57 -393895.608658] SPR radius for FAST iterations: 25 (autodetect)
[14:54:57 -393895.608658] Model parameter optimization (eps = 3.000000)
[14:55:20 -393681.424239] FAST spr round 1 (radius: 25)
[14:59:14 -354595.123562] FAST spr round 2 (radius: 25)
[15:02:11 -352866.650214] FAST spr round 3 (radius: 25)
[15:04:47 -352693.907308] FAST spr round 4 (radius: 25)
[15:07:07 -352685.891800] FAST spr round 5 (radius: 25)
[15:09:21 -352685.890554] Model parameter optimization (eps = 1.000000)
[15:09:39 -352681.043732] SLOW spr round 1 (radius: 5)
[15:12:51 -352622.507589] SLOW spr round 2 (radius: 5)
[15:15:53 -352604.521870] SLOW spr round 3 (radius: 5)
[15:18:45 -352604.521847] SLOW spr round 4 (radius: 10)
[15:21:40 -352604.521847] SLOW spr round 5 (radius: 15)
[15:26:51 -352604.521847] SLOW spr round 6 (radius: 20)
[15:35:13 -352604.521847] SLOW spr round 7 (radius: 25)
[15:47:26 -352604.521847] Model parameter optimization (eps = 0.100000)

[15:47:40] [worker #0] ML tree search #19, logLikelihood: -352603.895969

[16:09:00] [worker #1] ML tree search #20, logLikelihood: -352644.663384

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.181315,0.226801) (0.155136,0.349239) (0.351410,0.875980) (0.312139,1.912194) 
   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: -352583.123076

AIC score: 709176.246153 / AICc score: 8753236.246153 / BIC score: 718468.686035
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=761).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 55 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P18564/3_mltree/P18564.raxml.log

Analysis started: 08-Jul-2021 19:04:11 / finished: 09-Jul-2021 11:13:12

Elapsed time: 58141.061 seconds