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 03-Jul-2021 21:47:42 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/2_msa/O94823_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/3_mltree/O94823 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/2_msa/O94823_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 836 sites

WARNING: Sequences tr_B6Q2Z1_B6Q2Z1_TALMQ_441960 and tr_A0A093VR77_A0A093VR77_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_Q7SF11_Q7SF11_NEUCR_367110 and tr_G4U956_G4U956_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8NLF9_B8NLF9_ASPFN_332952 and tr_Q2U6U7_Q2U6U7_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NLF9_B8NLF9_ASPFN_332952 and tr_A0A1S9D963_A0A1S9D963_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_H2QRY1_H2QRY1_PANTR_9598 and tr_A0A2R9C7A7_A0A2R9C7A7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R0I2_H2R0I2_PANTR_9598 and sp_P98198_AT8B2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R0I2_H2R0I2_PANTR_9598 and tr_A0A2R9B168_A0A2R9B168_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7DFV6_K7DFV6_PANTR_9598 and tr_A0A2R8ZCR9_A0A2R8ZCR9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FX80_F9FX80_FUSOF_660025 and tr_A0A0D2XHL2_A0A0D2XHL2_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FX80_F9FX80_FUSOF_660025 and tr_X0D4J3_X0D4J3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FX80_F9FX80_FUSOF_660025 and tr_A0A2H3TH24_A0A2H3TH24_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FX80_F9FX80_FUSOF_660025 and tr_A0A2H3GRK5_A0A2H3GRK5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6HS06_C6HS06_AJECH_544712 and tr_F0UT68_F0UT68_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4UK20_J4UK20_BEAB2_655819 and tr_A0A0A2VHH0_A0A0A2VHH0_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4UK20_J4UK20_BEAB2_655819 and tr_A0A2N6N7W7_A0A2N6N7W7_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A158NID2_A0A158NID2_ATTCE_12957 and tr_A0A151HZZ7_A0A151HZZ7_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0GM05_A0A0E0GM05_ORYNI_4536 and tr_A0A0D9Z6Y1_A0A0D9Z6Y1_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2R0J1_A2R0J1_ASPNC_425011 and tr_G3XWE3_G3XWE3_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R0J1_A2R0J1_ASPNC_425011 and tr_A0A319A0H0_A0A319A0H0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7E886_F7E886_MACMU_9544 and tr_G7NUI6_G7NUI6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7E886_F7E886_MACMU_9544 and tr_A0A2I3MEJ8_A0A2I3MEJ8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7E886_F7E886_MACMU_9544 and tr_A0A2K5NGA7_A0A2K5NGA7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7E886_F7E886_MACMU_9544 and tr_A0A2K6CVY1_A0A2K6CVY1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7E886_F7E886_MACMU_9544 and tr_A0A2K5YW79_A0A2K5YW79_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XLC3_G7XLC3_ASPKW_1033177 and tr_A0A146EXE4_A0A146EXE4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9XAV4_F9XAV4_ZYMTI_336722 and tr_A0A1X7RT70_A0A1X7RT70_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2Y5G8_G2Y5G8_BOTF4_999810 and tr_M7V3L3_M7V3L3_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SE16_F2SE16_TRIRC_559305 and tr_A0A178EWN7_A0A178EWN7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_S0E5C9_S0E5C9_GIBF5_1279085 and tr_A0A365NF47_A0A365NF47_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A3B6HRZ1_A0A3B6HRZ1_WHEAT_4565 and tr_A0A3B6IQX1_A0A3B6IQX1_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A094ENB8_A0A094ENB8_9PEZI_1420912 and tr_A0A1B8GPY8_A0A1B8GPY8_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A094GDA2_A0A094GDA2_9PEZI_1420912 and tr_A0A1B8G6M2_A0A1B8G6M2_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4SQ72_V4SQ72_9ROSI_85681 and tr_A0A2H5MW75_A0A2H5MW75_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4U4B9_V4U4B9_9ROSI_85681 and tr_A0A2H5Q6W6_A0A2H5Q6W6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A117E3L2_A0A117E3L2_ASPNG_5061 and tr_A0A1L9MTA0_A0A1L9MTA0_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S4AM18_A0A1S4AM18_TOBAC_4097 and tr_A0A1U7WRE3_A0A1U7WRE3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2D0QMQ9_A0A2D0QMQ9_ICTPU_7998 and tr_A0A2D0QN06_A0A2D0QN06_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QMQ9_A0A2D0QMQ9_ICTPU_7998 and tr_A0A2D0QPN6_A0A2D0QPN6_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 38

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/O94823/3_mltree/O94823.raxml.reduced.phy

Alignment comprises 1 partitions and 836 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 836 / 836
Gaps: 2.22 %
Invariant sites: 1.32 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/3_mltree/O94823.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 / 209 / 16720
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1366390.901147] Initial branch length optimization
[00:00:09 -1160104.154145] Model parameter optimization (eps = 10.000000)
[00:00:53 -1158317.676177] AUTODETECT spr round 1 (radius: 5)
[00:04:04 -706098.299800] AUTODETECT spr round 2 (radius: 10)
[00:07:29 -479844.444857] AUTODETECT spr round 3 (radius: 15)
[00:10:58 -422450.924774] AUTODETECT spr round 4 (radius: 20)
[00:15:25 -381289.111594] AUTODETECT spr round 5 (radius: 25)
[00:19:42 -360012.195560] SPR radius for FAST iterations: 25 (autodetect)
[00:19:42 -360012.195560] Model parameter optimization (eps = 3.000000)
[00:20:06 -359933.024940] FAST spr round 1 (radius: 25)
[00:23:17 -283294.279637] FAST spr round 2 (radius: 25)
[00:25:38 -279342.915703] FAST spr round 3 (radius: 25)
[00:27:47 -279029.849263] FAST spr round 4 (radius: 25)
[00:29:40 -279024.775123] FAST spr round 5 (radius: 25)
[00:31:29 -279021.531424] FAST spr round 6 (radius: 25)
[00:33:16 -279021.531407] Model parameter optimization (eps = 1.000000)
[00:33:30 -279020.529476] SLOW spr round 1 (radius: 5)
[00:36:09 -278937.584019] SLOW spr round 2 (radius: 5)
[00:38:45 -278923.714871] SLOW spr round 3 (radius: 5)
[00:41:13 -278923.713707] SLOW spr round 4 (radius: 10)
[00:43:46 -278923.154829] SLOW spr round 5 (radius: 5)
[00:47:00 -278923.154633] SLOW spr round 6 (radius: 10)
[00:49:46 -278923.154632] SLOW spr round 7 (radius: 15)
[00:53:32 -278923.154630] SLOW spr round 8 (radius: 20)
[00:59:55 -278923.154628] SLOW spr round 9 (radius: 25)
[01:00:03] [worker #1] ML tree search #2, logLikelihood: -278907.267413
[01:08:05 -278923.154627] Model parameter optimization (eps = 0.100000)

[01:08:14] [worker #0] ML tree search #1, logLikelihood: -278923.040792

[01:08:15 -1379406.435672] Initial branch length optimization
[01:08:25 -1168624.422938] Model parameter optimization (eps = 10.000000)
[01:09:15 -1166692.099709] AUTODETECT spr round 1 (radius: 5)
[01:12:27 -716086.722345] AUTODETECT spr round 2 (radius: 10)
[01:15:57 -517744.928705] AUTODETECT spr round 3 (radius: 15)
[01:19:25 -434418.550039] AUTODETECT spr round 4 (radius: 20)
[01:23:48 -372603.238654] AUTODETECT spr round 5 (radius: 25)
[01:28:14 -353740.844772] SPR radius for FAST iterations: 25 (autodetect)
[01:28:14 -353740.844772] Model parameter optimization (eps = 3.000000)
[01:28:26 -353733.893175] FAST spr round 1 (radius: 25)
[01:31:42 -283118.807121] FAST spr round 2 (radius: 25)
[01:34:11 -279259.150334] FAST spr round 3 (radius: 25)
[01:36:17 -279125.060882] FAST spr round 4 (radius: 25)
[01:38:13 -279095.872673] FAST spr round 5 (radius: 25)
[01:40:05 -279091.421549] FAST spr round 6 (radius: 25)
[01:41:53 -279091.421539] Model parameter optimization (eps = 1.000000)
[01:42:09 -279050.377482] SLOW spr round 1 (radius: 5)
[01:44:55 -278931.797174] SLOW spr round 2 (radius: 5)
[01:47:27 -278925.315120] SLOW spr round 3 (radius: 5)
[01:49:57 -278924.426888] SLOW spr round 4 (radius: 5)
[01:52:24 -278922.865605] SLOW spr round 5 (radius: 5)
[01:54:49 -278922.865603] SLOW spr round 6 (radius: 10)
[01:57:21 -278920.236896] SLOW spr round 7 (radius: 5)
[02:00:36 -278919.895596] SLOW spr round 8 (radius: 5)
[02:03:22 -278919.895596] SLOW spr round 9 (radius: 10)
[02:05:58 -278919.895596] SLOW spr round 10 (radius: 15)
[02:09:53 -278919.895595] SLOW spr round 11 (radius: 20)
[02:10:18] [worker #1] ML tree search #4, logLikelihood: -278904.308805
[02:16:13 -278919.895595] SLOW spr round 12 (radius: 25)
[02:24:24 -278919.895595] Model parameter optimization (eps = 0.100000)

[02:24:36] [worker #0] ML tree search #3, logLikelihood: -278919.420626

[02:24:36 -1382904.804258] Initial branch length optimization
[02:24:46 -1176307.230364] Model parameter optimization (eps = 10.000000)
[02:25:42 -1174409.306975] AUTODETECT spr round 1 (radius: 5)
[02:28:49 -709463.000193] AUTODETECT spr round 2 (radius: 10)
[02:32:20 -505848.341963] AUTODETECT spr round 3 (radius: 15)
[02:36:00 -412240.628852] AUTODETECT spr round 4 (radius: 20)
[02:39:52 -354517.356081] AUTODETECT spr round 5 (radius: 25)
[02:44:10 -339801.618830] SPR radius for FAST iterations: 25 (autodetect)
[02:44:10 -339801.618830] Model parameter optimization (eps = 3.000000)
[02:44:23 -339791.278096] FAST spr round 1 (radius: 25)
[02:47:19 -281464.672233] FAST spr round 2 (radius: 25)
[02:49:36 -279308.064041] FAST spr round 3 (radius: 25)
[02:51:43 -279082.720296] FAST spr round 4 (radius: 25)
[02:53:38 -279057.020194] FAST spr round 5 (radius: 25)
[02:55:30 -279052.188015] FAST spr round 6 (radius: 25)
[02:57:19 -279047.233806] FAST spr round 7 (radius: 25)
[02:59:05 -279046.136408] FAST spr round 8 (radius: 25)
[03:00:51 -279046.136408] Model parameter optimization (eps = 1.000000)
[03:01:07 -279014.883121] SLOW spr round 1 (radius: 5)
[03:03:46 -278914.637434] SLOW spr round 2 (radius: 5)
[03:06:21 -278910.012762] SLOW spr round 3 (radius: 5)
[03:08:48 -278910.011703] SLOW spr round 4 (radius: 10)
[03:11:21 -278909.876538] SLOW spr round 5 (radius: 5)
[03:14:34 -278909.876417] SLOW spr round 6 (radius: 10)
[03:17:18 -278909.822382] SLOW spr round 7 (radius: 15)
[03:21:07 -278909.822381] SLOW spr round 8 (radius: 20)
[03:23:31] [worker #1] ML tree search #6, logLikelihood: -278904.462233
[03:27:32 -278909.822379] SLOW spr round 9 (radius: 25)
[03:35:44 -278909.822378] Model parameter optimization (eps = 0.100000)

[03:35:55] [worker #0] ML tree search #5, logLikelihood: -278909.404347

[03:35:55 -1387709.599087] Initial branch length optimization
[03:36:03 -1171632.056945] Model parameter optimization (eps = 10.000000)
[03:36:49 -1169900.076702] AUTODETECT spr round 1 (radius: 5)
[03:40:00 -693975.581421] AUTODETECT spr round 2 (radius: 10)
[03:43:22 -441927.201511] AUTODETECT spr round 3 (radius: 15)
[03:46:56 -364316.866294] AUTODETECT spr round 4 (radius: 20)
[03:50:56 -332082.299938] AUTODETECT spr round 5 (radius: 25)
[03:55:21 -324671.660043] SPR radius for FAST iterations: 25 (autodetect)
[03:55:21 -324671.660043] Model parameter optimization (eps = 3.000000)
[03:55:41 -324598.760082] FAST spr round 1 (radius: 25)
[03:58:36 -280846.988349] FAST spr round 2 (radius: 25)
[04:00:55 -279045.269592] FAST spr round 3 (radius: 25)
[04:03:02 -278998.806679] FAST spr round 4 (radius: 25)
[04:04:56 -278992.380701] FAST spr round 5 (radius: 25)
[04:06:45 -278989.359163] FAST spr round 6 (radius: 25)
[04:08:33 -278988.103802] FAST spr round 7 (radius: 25)
[04:10:19 -278988.103800] Model parameter optimization (eps = 1.000000)
[04:10:27 -278987.823560] SLOW spr round 1 (radius: 5)
[04:13:10 -278929.337967] SLOW spr round 2 (radius: 5)
[04:15:47 -278910.993350] SLOW spr round 3 (radius: 5)
[04:18:18 -278906.136030] SLOW spr round 4 (radius: 5)
[04:20:45 -278900.472736] SLOW spr round 5 (radius: 5)
[04:23:11 -278900.472658] SLOW spr round 6 (radius: 10)
[04:25:44 -278900.084912] SLOW spr round 7 (radius: 5)
[04:28:59 -278900.084445] SLOW spr round 8 (radius: 10)
[04:31:44 -278900.084444] SLOW spr round 9 (radius: 15)
[04:35:31 -278900.084443] SLOW spr round 10 (radius: 20)
[04:41:54 -278900.084441] SLOW spr round 11 (radius: 25)
[04:45:34] [worker #1] ML tree search #8, logLikelihood: -278900.000097
[04:49:56 -278900.084440] Model parameter optimization (eps = 0.100000)

[04:50:02] [worker #0] ML tree search #7, logLikelihood: -278900.020572

[04:50:03 -1376983.153544] Initial branch length optimization
[04:50:16 -1170754.134835] Model parameter optimization (eps = 10.000000)
[04:51:02 -1168681.236460] AUTODETECT spr round 1 (radius: 5)
[04:54:08 -701316.907726] AUTODETECT spr round 2 (radius: 10)
[04:57:34 -519175.649284] AUTODETECT spr round 3 (radius: 15)
[05:01:13 -393737.804402] AUTODETECT spr round 4 (radius: 20)
[05:05:09 -349047.510241] AUTODETECT spr round 5 (radius: 25)
[05:09:25 -334525.867946] SPR radius for FAST iterations: 25 (autodetect)
[05:09:25 -334525.867946] Model parameter optimization (eps = 3.000000)
[05:09:45 -334467.151894] FAST spr round 1 (radius: 25)
[05:12:54 -281036.885012] FAST spr round 2 (radius: 25)
[05:15:15 -279223.241015] FAST spr round 3 (radius: 25)
[05:17:21 -279008.187501] FAST spr round 4 (radius: 25)
[05:19:13 -278999.383610] FAST spr round 5 (radius: 25)
[05:21:00 -278999.382438] Model parameter optimization (eps = 1.000000)
[05:21:15 -278995.552594] SLOW spr round 1 (radius: 5)
[05:23:53 -278917.941391] SLOW spr round 2 (radius: 5)
[05:26:27 -278906.751842] SLOW spr round 3 (radius: 5)
[05:28:53 -278906.751515] SLOW spr round 4 (radius: 10)
[05:31:25 -278904.848208] SLOW spr round 5 (radius: 5)
[05:34:40 -278904.506508] SLOW spr round 6 (radius: 5)
[05:37:27 -278904.506404] SLOW spr round 7 (radius: 10)
[05:40:02 -278904.437739] SLOW spr round 8 (radius: 15)
[05:43:55 -278904.437674] SLOW spr round 9 (radius: 20)
[05:50:12 -278904.437615] SLOW spr round 10 (radius: 25)
[05:58:19 -278904.437567] Model parameter optimization (eps = 0.100000)

[05:58:33] [worker #0] ML tree search #9, logLikelihood: -278904.054711

[05:58:33 -1370832.869323] Initial branch length optimization
[05:58:44 -1164827.550255] Model parameter optimization (eps = 10.000000)
[05:59:38 -1162916.465287] AUTODETECT spr round 1 (radius: 5)
[06:00:04] [worker #1] ML tree search #10, logLikelihood: -278902.659389
[06:02:50 -699464.616084] AUTODETECT spr round 2 (radius: 10)
[06:06:07 -501038.776585] AUTODETECT spr round 3 (radius: 15)
[06:09:37 -393918.506095] AUTODETECT spr round 4 (radius: 20)
[06:13:31 -343456.414600] AUTODETECT spr round 5 (radius: 25)
[06:18:14 -335779.788217] SPR radius for FAST iterations: 25 (autodetect)
[06:18:14 -335779.788217] Model parameter optimization (eps = 3.000000)
[06:18:38 -335703.511079] FAST spr round 1 (radius: 25)
[06:21:39 -281766.492802] FAST spr round 2 (radius: 25)
[06:24:01 -279136.247504] FAST spr round 3 (radius: 25)
[06:26:12 -278999.414690] FAST spr round 4 (radius: 25)
[06:28:08 -278985.414043] FAST spr round 5 (radius: 25)
[06:29:57 -278985.414039] Model parameter optimization (eps = 1.000000)
[06:30:10 -278982.692890] SLOW spr round 1 (radius: 5)
[06:32:55 -278927.905514] SLOW spr round 2 (radius: 5)
[06:35:28 -278922.755122] SLOW spr round 3 (radius: 5)
[06:37:55 -278921.171730] SLOW spr round 4 (radius: 5)
[06:40:21 -278921.171270] SLOW spr round 5 (radius: 10)
[06:42:53 -278919.380813] SLOW spr round 6 (radius: 5)
[06:46:07 -278919.380790] SLOW spr round 7 (radius: 10)
[06:48:53 -278919.194912] SLOW spr round 8 (radius: 5)
[06:52:04 -278919.194504] SLOW spr round 9 (radius: 10)
[06:54:45 -278919.194502] SLOW spr round 10 (radius: 15)
[06:58:34 -278919.194501] SLOW spr round 11 (radius: 20)
[07:04:58 -278919.194499] SLOW spr round 12 (radius: 25)
[07:12:13] [worker #1] ML tree search #12, logLikelihood: -278893.340017
[07:13:06 -278919.194498] Model parameter optimization (eps = 0.100000)

[07:13:18] [worker #0] ML tree search #11, logLikelihood: -278918.868990

[07:13:18 -1373111.488226] Initial branch length optimization
[07:13:28 -1164175.076579] Model parameter optimization (eps = 10.000000)
[07:14:20 -1162033.962115] AUTODETECT spr round 1 (radius: 5)
[07:17:32 -719489.899375] AUTODETECT spr round 2 (radius: 10)
[07:21:02 -521649.165474] AUTODETECT spr round 3 (radius: 15)
[07:24:47 -414506.598209] AUTODETECT spr round 4 (radius: 20)
[07:29:00 -375639.359364] AUTODETECT spr round 5 (radius: 25)
[07:33:04 -350848.881367] SPR radius for FAST iterations: 25 (autodetect)
[07:33:04 -350848.881367] Model parameter optimization (eps = 3.000000)
[07:33:14 -350837.632493] FAST spr round 1 (radius: 25)
[07:36:24 -282858.246628] FAST spr round 2 (radius: 25)
[07:38:53 -279330.106453] FAST spr round 3 (radius: 25)
[07:41:10 -279088.541067] FAST spr round 4 (radius: 25)
[07:43:17 -279040.130506] FAST spr round 5 (radius: 25)
[07:45:08 -279028.422161] FAST spr round 6 (radius: 25)
[07:47:01 -279022.823615] FAST spr round 7 (radius: 25)
[07:48:46 -279022.823418] Model parameter optimization (eps = 1.000000)
[07:49:03 -278982.990899] SLOW spr round 1 (radius: 5)
[07:51:45 -278919.501049] SLOW spr round 2 (radius: 5)
[07:54:18 -278916.894350] SLOW spr round 3 (radius: 5)
[07:56:46 -278916.894096] SLOW spr round 4 (radius: 10)
[07:59:20 -278916.893964] SLOW spr round 5 (radius: 15)
[08:03:17 -278916.893844] SLOW spr round 6 (radius: 20)
[08:09:33 -278916.893733] SLOW spr round 7 (radius: 25)
[08:17:45 -278916.893632] Model parameter optimization (eps = 0.100000)

[08:17:59] [worker #0] ML tree search #13, logLikelihood: -278916.452983

[08:17:59 -1383429.699388] Initial branch length optimization
[08:18:07 -1173922.995792] Model parameter optimization (eps = 10.000000)
[08:19:00 -1172131.733842] AUTODETECT spr round 1 (radius: 5)
[08:22:12 -713829.623878] AUTODETECT spr round 2 (radius: 10)
[08:23:25] [worker #1] ML tree search #14, logLikelihood: -278927.291845
[08:25:37 -478905.533277] AUTODETECT spr round 3 (radius: 15)
[08:29:14 -386297.108458] AUTODETECT spr round 4 (radius: 20)
[08:33:12 -350225.435102] AUTODETECT spr round 5 (radius: 25)
[08:37:04 -343657.795397] SPR radius for FAST iterations: 25 (autodetect)
[08:37:04 -343657.795397] Model parameter optimization (eps = 3.000000)
[08:37:39 -343601.559063] FAST spr round 1 (radius: 25)
[08:40:54 -285613.903151] FAST spr round 2 (radius: 25)
[08:43:18 -279541.818723] FAST spr round 3 (radius: 25)
[08:45:32 -279108.733656] FAST spr round 4 (radius: 25)
[08:47:35 -279004.713037] FAST spr round 5 (radius: 25)
[08:49:28 -279000.890373] FAST spr round 6 (radius: 25)
[08:51:17 -279000.890372] Model parameter optimization (eps = 1.000000)
[08:51:30 -278998.560724] SLOW spr round 1 (radius: 5)
[08:54:19 -278921.278526] SLOW spr round 2 (radius: 5)
[08:56:59 -278912.470468] SLOW spr round 3 (radius: 5)
[08:59:28 -278904.576844] SLOW spr round 4 (radius: 5)
[09:01:53 -278904.576843] SLOW spr round 5 (radius: 10)
[09:04:25 -278902.277897] SLOW spr round 6 (radius: 5)
[09:07:41 -278902.277701] SLOW spr round 7 (radius: 10)
[09:10:25 -278902.089324] SLOW spr round 8 (radius: 5)
[09:13:36 -278902.088918] SLOW spr round 9 (radius: 10)
[09:16:17 -278902.088918] SLOW spr round 10 (radius: 15)
[09:20:06 -278902.088918] SLOW spr round 11 (radius: 20)
[09:26:26 -278902.088918] SLOW spr round 12 (radius: 25)
[09:26:44] [worker #1] ML tree search #16, logLikelihood: -278908.623184
[09:34:37 -278902.088918] Model parameter optimization (eps = 0.100000)

[09:34:49] [worker #0] ML tree search #15, logLikelihood: -278901.888113

[09:34:49 -1373322.897023] Initial branch length optimization
[09:34:58 -1166264.069408] Model parameter optimization (eps = 10.000000)
[09:35:47 -1164343.093286] AUTODETECT spr round 1 (radius: 5)
[09:38:55 -700324.042656] AUTODETECT spr round 2 (radius: 10)
[09:42:13 -509189.376227] AUTODETECT spr round 3 (radius: 15)
[09:45:49 -388520.352060] AUTODETECT spr round 4 (radius: 20)
[09:49:18 -343163.112885] AUTODETECT spr round 5 (radius: 25)
[09:53:20 -332685.541002] SPR radius for FAST iterations: 25 (autodetect)
[09:53:20 -332685.541002] Model parameter optimization (eps = 3.000000)
[09:53:43 -332644.709996] FAST spr round 1 (radius: 25)
[09:56:41 -283175.112176] FAST spr round 2 (radius: 25)
[09:59:01 -279325.707062] FAST spr round 3 (radius: 25)
[10:01:05 -279106.729700] FAST spr round 4 (radius: 25)
[10:02:57 -279005.601130] FAST spr round 5 (radius: 25)
[10:04:45 -279005.338405] FAST spr round 6 (radius: 25)
[10:06:30 -279005.338399] Model parameter optimization (eps = 1.000000)
[10:06:44 -279002.384922] SLOW spr round 1 (radius: 5)
[10:09:25 -278906.184007] SLOW spr round 2 (radius: 5)
[10:11:58 -278901.348029] SLOW spr round 3 (radius: 5)
[10:14:27 -278901.133180] SLOW spr round 4 (radius: 5)
[10:16:53 -278901.133157] SLOW spr round 5 (radius: 10)
[10:19:23 -278901.133155] SLOW spr round 6 (radius: 15)
[10:23:16 -278901.133155] SLOW spr round 7 (radius: 20)
[10:29:31 -278901.133155] SLOW spr round 8 (radius: 25)
[10:34:26] [worker #1] ML tree search #18, logLikelihood: -278905.317444
[10:37:34 -278901.133155] Model parameter optimization (eps = 0.100000)

[10:37:39] [worker #0] ML tree search #17, logLikelihood: -278901.057249

[10:37:39 -1368877.085553] Initial branch length optimization
[10:37:50 -1155763.033877] Model parameter optimization (eps = 10.000000)
[10:39:19 -1153676.847521] AUTODETECT spr round 1 (radius: 5)
[10:42:32 -718588.034576] AUTODETECT spr round 2 (radius: 10)
[10:45:59 -507680.322048] AUTODETECT spr round 3 (radius: 15)
[10:49:31 -418526.187470] AUTODETECT spr round 4 (radius: 20)
[10:53:21 -365973.750897] AUTODETECT spr round 5 (radius: 25)
[10:57:50 -347508.329883] SPR radius for FAST iterations: 25 (autodetect)
[10:57:50 -347508.329883] Model parameter optimization (eps = 3.000000)
[10:58:10 -347467.619803] FAST spr round 1 (radius: 25)
[11:00:58 -282203.071882] FAST spr round 2 (radius: 25)
[11:03:06 -279323.714280] FAST spr round 3 (radius: 25)
[11:05:05 -279059.681998] FAST spr round 4 (radius: 25)
[11:06:51 -279050.515935] FAST spr round 5 (radius: 25)
[11:08:34 -279044.973650] FAST spr round 6 (radius: 25)
[11:10:13 -279044.973620] Model parameter optimization (eps = 1.000000)
[11:10:25 -279043.933798] SLOW spr round 1 (radius: 5)
[11:12:58 -278917.932775] SLOW spr round 2 (radius: 5)
[11:15:22 -278906.667001] SLOW spr round 3 (radius: 5)
[11:17:37 -278906.630111] SLOW spr round 4 (radius: 10)
[11:20:00 -278906.630091] SLOW spr round 5 (radius: 15)
[11:23:49 -278906.630089] SLOW spr round 6 (radius: 20)
[11:29:48 -278906.630087] SLOW spr round 7 (radius: 25)
[11:33:56] [worker #1] ML tree search #20, logLikelihood: -278916.727731
[11:38:03 -278906.630086] Model parameter optimization (eps = 0.100000)

[11:38:12] [worker #0] ML tree search #19, logLikelihood: -278906.488910


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.269814,0.307717) (0.320685,0.554869) (0.290623,1.379295) (0.118878,2.844765) 
   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: -278893.340017

AIC score: 561796.680033 / AICc score: 8605856.680033 / BIC score: 571277.580403
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=836).
         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/O94823/3_mltree/O94823.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/3_mltree/O94823.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/3_mltree/O94823.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94823/3_mltree/O94823.raxml.log

Analysis started: 03-Jul-2021 21:47:42 / finished: 04-Jul-2021 09:25:55

Elapsed time: 41892.764 seconds

Consumed energy: 3779.939 Wh (= 19 km in an electric car, or 94 km with an e-scooter!)