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 02-Jul-2021 11:09:11 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/2_msa/Q96RP9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9 --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/Q96RP9/2_msa/Q96RP9_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 799 sites

WARNING: Sequences sp_B4Q5D5_EFGM_DROSI_7240 and sp_B4HY41_EFGM_DROSE_7238 are exactly identical!
WARNING: Sequences sp_Q1DLM0_EFGM_COCIM_246410 and tr_A0A0J6YHD4_A0A0J6YHD4_COCIT_404692 are exactly identical!
WARNING: Sequences sp_B2WBM8_EFGM_PYRTR_426418 and tr_A0A2W1ETP0_A0A2W1ETP0_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3S1S5_G3S1S5_GORGO_9595 and tr_H2R7Y8_H2R7Y8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S1S5_G3S1S5_GORGO_9595 and tr_A0A2R9AW37_A0A2R9AW37_PANPA_9597 are exactly identical!
WARNING: Sequences sp_B8N9M2_EFGM_ASPFN_332952 and sp_Q2UGQ2_EFGM_ASPOR_510516 are exactly identical!
WARNING: Sequences sp_B8N9M2_EFGM_ASPFN_332952 and tr_A0A1S9DZ16_A0A1S9DZ16_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UFS4_A0A179UFS4_BLAGS_559298 and tr_C5GFF4_C5GFF4_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A0D2Y4X0_A0A0D2Y4X0_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_X0CSW1_X0CSW1_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A2H3SUK9_A0A2H3SUK9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A2H3HRX7_A0A2H3HRX7_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6H211_C6H211_AJECH_544712 and tr_F0U4G6_F0U4G6_AJEC8_544711 are exactly identical!
WARNING: Sequences sp_A2QI77_EFGM_ASPNC_425011 and tr_G3Y8R9_G3Y8R9_ASPNA_380704 are exactly identical!
WARNING: Sequences sp_A2QI77_EFGM_ASPNC_425011 and tr_A0A319AHG1_A0A319AHG1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7X7E8_G7X7E8_ASPKW_1033177 and tr_A0A146FI78_A0A146FI78_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2XVY3_A2XVY3_ORYSI_39946 and tr_A0A0E0PC33_A0A0E0PC33_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1PCT5_I1PCT5_ORYGL_4538 and tr_A0A0D3FKH0_A0A0D3FKH0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PCT5_I1PCT5_ORYGL_4538 and sp_Q9FE64_EFGM_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1PNF0_I1PNF0_ORYGL_4538 and tr_A0A0D3FYE6_A0A0D3FYE6_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PNF0_I1PNF0_ORYGL_4538 and tr_A0A0D9ZNL3_A0A0D9ZNL3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_G2Y8S3_G2Y8S3_BOTF4_999810 and tr_M7U4F2_M7U4F2_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SWJ7_F2SWJ7_TRIRC_559305 and tr_A0A178EYS4_A0A178EYS4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_S0DKK9_S0DKK9_GIBF5_1279085 and tr_A0A365MSI9_A0A365MSI9_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_V2XFK5_V2XFK5_MONRO_1381753 and tr_A0A0W0G0G9_A0A0W0G0G9_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QVP1_W2QVP1_PHYPN_761204 and tr_W2JZH9_W2JZH9_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067H188_A0A067H188_CITSI_2711 and tr_V4U8R6_V4U8R6_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067H188_A0A067H188_CITSI_2711 and tr_A0A2H5NPL6_A0A2H5NPL6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A164P9D4_A0A164P9D4_9HOMO_1314777 and tr_A0A165YQ21_A0A165YQ21_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1U8EDZ1_A0A1U8EDZ1_CAPAN_4072 and tr_A0A2G3DJA4_A0A2G3DJA4_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 30

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/Q96RP9/3_mltree/Q96RP9.raxml.reduced.phy

Alignment comprises 1 partitions and 799 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 799 / 799
Gaps: 7.86 %
Invariant sites: 2.63 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.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 / 200 / 16000
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1025002.492266] Initial branch length optimization
[00:00:07 -879561.584553] Model parameter optimization (eps = 10.000000)
[00:00:57 -878120.582836] AUTODETECT spr round 1 (radius: 5)
[00:04:09 -610067.394701] AUTODETECT spr round 2 (radius: 10)
[00:07:58 -446552.772088] AUTODETECT spr round 3 (radius: 15)
[00:12:10 -370024.810089] AUTODETECT spr round 4 (radius: 20)
[00:16:58 -344005.952025] AUTODETECT spr round 5 (radius: 25)
[00:22:42 -340757.251382] SPR radius for FAST iterations: 25 (autodetect)
[00:22:42 -340757.251382] Model parameter optimization (eps = 3.000000)
[00:23:07 -340680.782211] FAST spr round 1 (radius: 25)
[00:26:56 -298920.213869] FAST spr round 2 (radius: 25)
[00:29:44 -297600.837971] FAST spr round 3 (radius: 25)
[00:32:19 -297503.459323] FAST spr round 4 (radius: 25)
[00:34:38 -297475.896226] FAST spr round 5 (radius: 25)
[00:36:50 -297457.484396] FAST spr round 6 (radius: 25)
[00:38:57 -297457.484303] Model parameter optimization (eps = 1.000000)
[00:39:09 -297455.203753] SLOW spr round 1 (radius: 5)
[00:42:22 -297366.216114] SLOW spr round 2 (radius: 5)
[00:45:30 -297333.307957] SLOW spr round 3 (radius: 5)
[00:48:27 -297328.311435] SLOW spr round 4 (radius: 5)
[00:51:22 -297321.745073] SLOW spr round 5 (radius: 5)
[00:54:19 -297321.744974] SLOW spr round 6 (radius: 10)
[00:57:17 -297321.744973] SLOW spr round 7 (radius: 15)
[01:02:28 -297321.744973] SLOW spr round 8 (radius: 20)
[01:10:02 -297321.744973] SLOW spr round 9 (radius: 25)
[01:18:44] [worker #1] ML tree search #2, logLikelihood: -297308.560238
[01:19:46 -297321.744973] Model parameter optimization (eps = 0.100000)

[01:19:54] [worker #0] ML tree search #1, logLikelihood: -297321.659691

[01:19:54 -1023838.707763] Initial branch length optimization
[01:20:00 -881294.386208] Model parameter optimization (eps = 10.000000)
[01:20:47 -879640.566360] AUTODETECT spr round 1 (radius: 5)
[01:24:02 -617007.660077] AUTODETECT spr round 2 (radius: 10)
[01:28:09 -437434.103275] AUTODETECT spr round 3 (radius: 15)
[01:32:15 -382040.157680] AUTODETECT spr round 4 (radius: 20)
[01:37:26 -342991.724715] AUTODETECT spr round 5 (radius: 25)
[01:44:19 -336408.907053] SPR radius for FAST iterations: 25 (autodetect)
[01:44:19 -336408.907053] Model parameter optimization (eps = 3.000000)
[01:44:27 -336408.454789] FAST spr round 1 (radius: 25)
[01:48:35 -298668.371290] FAST spr round 2 (radius: 25)
[01:51:48 -297564.074932] FAST spr round 3 (radius: 25)
[01:54:33 -297491.981781] FAST spr round 4 (radius: 25)
[01:56:51 -297488.573335] FAST spr round 5 (radius: 25)
[01:59:05 -297487.098508] FAST spr round 6 (radius: 25)
[02:01:15 -297487.098284] Model parameter optimization (eps = 1.000000)
[02:01:35 -297386.386237] SLOW spr round 1 (radius: 5)
[02:05:02 -297317.374081] SLOW spr round 2 (radius: 5)
[02:08:21 -297308.611756] SLOW spr round 3 (radius: 5)
[02:11:25 -297308.609014] SLOW spr round 4 (radius: 10)
[02:14:33 -297308.607146] SLOW spr round 5 (radius: 15)
[02:19:44 -297308.605619] SLOW spr round 6 (radius: 20)
[02:27:22 -297308.605214] SLOW spr round 7 (radius: 25)
[02:37:31 -297308.604992] Model parameter optimization (eps = 0.100000)

[02:37:39] [worker #0] ML tree search #3, logLikelihood: -297308.554528

[02:37:39 -1028729.627720] Initial branch length optimization
[02:37:46 -882716.153785] Model parameter optimization (eps = 10.000000)
[02:38:40 -881216.382288] AUTODETECT spr round 1 (radius: 5)
[02:42:06 -613927.698555] AUTODETECT spr round 2 (radius: 10)
[02:43:29] [worker #1] ML tree search #4, logLikelihood: -297311.489941
[02:46:16 -450926.743368] AUTODETECT spr round 3 (radius: 15)
[02:51:04 -382239.655452] AUTODETECT spr round 4 (radius: 20)
[02:55:57 -350574.811224] AUTODETECT spr round 5 (radius: 25)
[03:01:11 -343042.104372] SPR radius for FAST iterations: 25 (autodetect)
[03:01:11 -343042.104372] Model parameter optimization (eps = 3.000000)
[03:01:36 -342936.867569] FAST spr round 1 (radius: 25)
[03:05:46 -298718.390833] FAST spr round 2 (radius: 25)
[03:08:41 -297464.288363] FAST spr round 3 (radius: 25)
[03:11:22 -297385.832788] FAST spr round 4 (radius: 25)
[03:13:43 -297378.894448] FAST spr round 5 (radius: 25)
[03:15:56 -297378.894115] Model parameter optimization (eps = 1.000000)
[03:16:09 -297376.127198] SLOW spr round 1 (radius: 5)
[03:19:39 -297329.257966] SLOW spr round 2 (radius: 5)
[03:22:57 -297322.593599] SLOW spr round 3 (radius: 5)
[03:26:03 -297322.591312] SLOW spr round 4 (radius: 10)
[03:29:14 -297315.147672] SLOW spr round 5 (radius: 5)
[03:33:14 -297310.305589] SLOW spr round 6 (radius: 5)
[03:36:40 -297310.305348] SLOW spr round 7 (radius: 10)
[03:39:53 -297310.305154] SLOW spr round 8 (radius: 15)
[03:45:06 -297310.304981] SLOW spr round 9 (radius: 20)
[03:53:08 -297310.304972] SLOW spr round 10 (radius: 25)
[04:03:09 -297310.304972] Model parameter optimization (eps = 0.100000)

[04:03:21] [worker #0] ML tree search #5, logLikelihood: -297310.137993

[04:03:21 -1018779.723239] Initial branch length optimization
[04:03:27 -879923.368769] Model parameter optimization (eps = 10.000000)
[04:04:12 -878316.007879] AUTODETECT spr round 1 (radius: 5)
[04:07:30 -602533.560138] AUTODETECT spr round 2 (radius: 10)
[04:11:28 -456800.798278] AUTODETECT spr round 3 (radius: 15)
[04:11:36] [worker #1] ML tree search #6, logLikelihood: -297299.872754
[04:15:48 -412306.744185] AUTODETECT spr round 4 (radius: 20)
[04:20:37 -365298.405389] AUTODETECT spr round 5 (radius: 25)
[04:25:35 -351063.732130] SPR radius for FAST iterations: 25 (autodetect)
[04:25:35 -351063.732130] Model parameter optimization (eps = 3.000000)
[04:26:03 -350978.054842] FAST spr round 1 (radius: 25)
[04:30:20 -299628.367521] FAST spr round 2 (radius: 25)
[04:33:25 -297541.993452] FAST spr round 3 (radius: 25)
[04:36:11 -297390.617375] FAST spr round 4 (radius: 25)
[04:38:32 -297382.193761] FAST spr round 5 (radius: 25)
[04:40:50 -297382.193362] Model parameter optimization (eps = 1.000000)
[04:41:06 -297376.970741] SLOW spr round 1 (radius: 5)
[04:44:35 -297304.868872] SLOW spr round 2 (radius: 5)
[04:47:41 -297301.663646] SLOW spr round 3 (radius: 5)
[04:50:44 -297301.663416] SLOW spr round 4 (radius: 10)
[04:53:52 -297301.663200] SLOW spr round 5 (radius: 15)
[04:59:11 -297301.663188] SLOW spr round 6 (radius: 20)
[05:07:27 -297301.663188] SLOW spr round 7 (radius: 25)
[05:17:57 -297301.663188] Model parameter optimization (eps = 0.100000)

[05:18:03] [worker #0] ML tree search #7, logLikelihood: -297301.648219

[05:18:03 -1030839.749963] Initial branch length optimization
[05:18:09 -885046.647553] Model parameter optimization (eps = 10.000000)
[05:18:51 -883602.771863] AUTODETECT spr round 1 (radius: 5)
[05:22:17 -622932.234114] AUTODETECT spr round 2 (radius: 10)
[05:26:39 -450471.748248] AUTODETECT spr round 3 (radius: 15)
[05:31:10 -382174.067941] AUTODETECT spr round 4 (radius: 20)
[05:35:33] [worker #1] ML tree search #8, logLikelihood: -297297.894245
[05:35:49 -346180.416164] AUTODETECT spr round 5 (radius: 25)
[05:40:33 -338695.283385] SPR radius for FAST iterations: 25 (autodetect)
[05:40:33 -338695.283385] Model parameter optimization (eps = 3.000000)
[05:41:03 -338589.419139] FAST spr round 1 (radius: 25)
[05:45:07 -299044.513727] FAST spr round 2 (radius: 25)
[05:48:10 -297508.599683] FAST spr round 3 (radius: 25)
[05:50:44 -297436.198140] FAST spr round 4 (radius: 25)
[05:53:00 -297436.197812] Model parameter optimization (eps = 1.000000)
[05:53:15 -297432.710217] SLOW spr round 1 (radius: 5)
[05:57:00 -297338.994578] SLOW spr round 2 (radius: 5)
[06:00:19 -297317.402127] SLOW spr round 3 (radius: 5)
[06:03:25 -297309.195350] SLOW spr round 4 (radius: 5)
[06:06:24 -297309.195349] SLOW spr round 5 (radius: 10)
[06:09:34 -297306.466477] SLOW spr round 6 (radius: 5)
[06:13:44 -297303.269832] SLOW spr round 7 (radius: 5)
[06:17:13 -297303.251599] SLOW spr round 8 (radius: 10)
[06:20:33 -297303.251597] SLOW spr round 9 (radius: 15)
[06:25:43 -297303.251597] SLOW spr round 10 (radius: 20)
[06:33:41 -297303.251597] SLOW spr round 11 (radius: 25)
[06:43:59 -297303.251597] Model parameter optimization (eps = 0.100000)

[06:44:16] [worker #0] ML tree search #9, logLikelihood: -297303.092013

[06:44:17 -1031905.993386] Initial branch length optimization
[06:44:22 -885142.679578] Model parameter optimization (eps = 10.000000)
[06:45:15 -883647.423085] AUTODETECT spr round 1 (radius: 5)
[06:48:35 -605190.519071] AUTODETECT spr round 2 (radius: 10)
[06:52:26 -456526.839870] AUTODETECT spr round 3 (radius: 15)
[06:57:07 -385076.902838] AUTODETECT spr round 4 (radius: 20)
[07:02:22 -352934.399911] AUTODETECT spr round 5 (radius: 25)
[07:06:15] [worker #1] ML tree search #10, logLikelihood: -297294.411604
[07:08:25 -349065.171586] SPR radius for FAST iterations: 25 (autodetect)
[07:08:25 -349065.171586] Model parameter optimization (eps = 3.000000)
[07:08:52 -348979.957752] FAST spr round 1 (radius: 25)
[07:13:06 -301559.767844] FAST spr round 2 (radius: 25)
[07:16:09 -298620.505911] FAST spr round 3 (radius: 25)
[07:18:51 -297441.307720] FAST spr round 4 (radius: 25)
[07:21:15 -297426.638827] FAST spr round 5 (radius: 25)
[07:23:32 -297426.638272] Model parameter optimization (eps = 1.000000)
[07:23:49 -297423.778696] SLOW spr round 1 (radius: 5)
[07:27:16 -297322.084531] SLOW spr round 2 (radius: 5)
[07:30:36 -297305.839473] SLOW spr round 3 (radius: 5)
[07:33:46 -297305.337070] SLOW spr round 4 (radius: 5)
[07:36:45 -297305.336746] SLOW spr round 5 (radius: 10)
[07:39:55 -297304.627976] SLOW spr round 6 (radius: 5)
[07:43:56 -297303.636354] SLOW spr round 7 (radius: 5)
[07:47:24 -297303.636336] SLOW spr round 8 (radius: 10)
[07:50:39 -297303.636336] SLOW spr round 9 (radius: 15)
[07:55:57 -297303.636336] SLOW spr round 10 (radius: 20)
[08:03:58 -297303.636336] SLOW spr round 11 (radius: 25)
[08:14:22 -297303.636336] Model parameter optimization (eps = 0.100000)

[08:14:35] [worker #0] ML tree search #11, logLikelihood: -297303.480988

[08:14:35 -1026088.409717] Initial branch length optimization
[08:14:42 -882422.326874] Model parameter optimization (eps = 10.000000)
[08:15:26 -880842.021830] AUTODETECT spr round 1 (radius: 5)
[08:18:34 -606578.354049] AUTODETECT spr round 2 (radius: 10)
[08:21:43 -428957.365610] AUTODETECT spr round 3 (radius: 15)
[08:23:27] [worker #1] ML tree search #12, logLikelihood: -297317.243867
[08:25:02 -353473.242760] AUTODETECT spr round 4 (radius: 20)
[08:28:50 -335141.286582] AUTODETECT spr round 5 (radius: 25)
[08:33:01 -333852.029034] SPR radius for FAST iterations: 25 (autodetect)
[08:33:01 -333852.029034] Model parameter optimization (eps = 3.000000)
[08:33:29 -333721.268630] FAST spr round 1 (radius: 25)
[08:36:56 -298867.722980] FAST spr round 2 (radius: 25)
[08:39:43 -297521.002028] FAST spr round 3 (radius: 25)
[08:42:06 -297386.454455] FAST spr round 4 (radius: 25)
[08:44:02 -297385.269864] FAST spr round 5 (radius: 25)
[08:45:56 -297385.269819] Model parameter optimization (eps = 1.000000)
[08:46:03 -297384.811885] SLOW spr round 1 (radius: 5)
[08:49:08 -297326.951720] SLOW spr round 2 (radius: 5)
[08:51:57 -297318.747006] SLOW spr round 3 (radius: 5)
[08:54:41 -297315.515450] SLOW spr round 4 (radius: 5)
[08:57:26 -297315.515373] SLOW spr round 5 (radius: 10)
[09:00:19 -297315.515371] SLOW spr round 6 (radius: 15)
[09:05:03 -297315.515370] SLOW spr round 7 (radius: 20)
[09:12:23 -297315.515370] SLOW spr round 8 (radius: 25)
[09:21:54 -297315.515369] Model parameter optimization (eps = 0.100000)

[09:22:00] [worker #0] ML tree search #13, logLikelihood: -297315.420914

[09:22:00 -1025405.033100] Initial branch length optimization
[09:22:06 -883428.280821] Model parameter optimization (eps = 10.000000)
[09:22:49 -881917.617097] AUTODETECT spr round 1 (radius: 5)
[09:25:52 -624415.266017] AUTODETECT spr round 2 (radius: 10)
[09:29:47 -461621.462709] AUTODETECT spr round 3 (radius: 15)
[09:31:32] [worker #1] ML tree search #14, logLikelihood: -297301.796653
[09:33:54 -377115.247718] AUTODETECT spr round 4 (radius: 20)
[09:38:49 -350155.743009] AUTODETECT spr round 5 (radius: 25)
[09:44:23 -346757.400291] SPR radius for FAST iterations: 25 (autodetect)
[09:44:23 -346757.400291] Model parameter optimization (eps = 3.000000)
[09:44:46 -346645.920440] FAST spr round 1 (radius: 25)
[09:48:27 -299082.249119] FAST spr round 2 (radius: 25)
[09:51:13 -297626.533463] FAST spr round 3 (radius: 25)
[09:53:32 -297492.592505] FAST spr round 4 (radius: 25)
[09:55:40 -297426.324394] FAST spr round 5 (radius: 25)
[09:57:42 -297425.097013] FAST spr round 6 (radius: 25)
[09:59:34 -297425.096636] Model parameter optimization (eps = 1.000000)
[09:59:44 -297422.817282] SLOW spr round 1 (radius: 5)
[10:02:48 -297328.279286] SLOW spr round 2 (radius: 5)
[10:05:41 -297317.638192] SLOW spr round 3 (radius: 5)
[10:08:26 -297317.635933] SLOW spr round 4 (radius: 10)
[10:11:15 -297317.634248] SLOW spr round 5 (radius: 15)
[10:16:02 -297317.632839] SLOW spr round 6 (radius: 20)
[10:23:27 -297317.632600] SLOW spr round 7 (radius: 25)
[10:32:44 -297317.632465] Model parameter optimization (eps = 0.100000)

[10:32:50] [worker #0] ML tree search #15, logLikelihood: -297317.605228

[10:32:50 -1032816.255497] Initial branch length optimization
[10:32:54 -885213.314706] Model parameter optimization (eps = 10.000000)
[10:33:39 -883726.011518] AUTODETECT spr round 1 (radius: 5)
[10:36:55 -619218.375103] AUTODETECT spr round 2 (radius: 10)
[10:40:41 -455697.904595] AUTODETECT spr round 3 (radius: 15)
[10:44:53 -389903.590991] AUTODETECT spr round 4 (radius: 20)
[10:48:38 -353025.338050] AUTODETECT spr round 5 (radius: 25)
[10:53:16 -346874.091031] SPR radius for FAST iterations: 25 (autodetect)
[10:53:16 -346874.091031] Model parameter optimization (eps = 3.000000)
[10:53:22 -346873.187135] FAST spr round 1 (radius: 25)
[10:57:14 -299166.760003] FAST spr round 2 (radius: 25)
[10:58:14] [worker #1] ML tree search #16, logLikelihood: -297296.644192
[11:00:05 -297554.279616] FAST spr round 3 (radius: 25)
[11:02:28 -297467.511170] FAST spr round 4 (radius: 25)
[11:04:35 -297456.340135] FAST spr round 5 (radius: 25)
[11:06:38 -297454.487359] FAST spr round 6 (radius: 25)
[11:08:39 -297454.486839] Model parameter optimization (eps = 1.000000)
[11:08:58 -297377.887626] SLOW spr round 1 (radius: 5)
[11:12:07 -297320.489448] SLOW spr round 2 (radius: 5)
[11:15:01 -297305.262928] SLOW spr round 3 (radius: 5)
[11:17:49 -297303.164129] SLOW spr round 4 (radius: 5)
[11:20:27 -297303.162598] SLOW spr round 5 (radius: 10)
[11:23:14 -297303.161852] SLOW spr round 6 (radius: 15)
[11:28:00 -297303.161851] SLOW spr round 7 (radius: 20)
[11:35:12 -297303.161850] SLOW spr round 8 (radius: 25)
[11:44:19 -297303.161850] Model parameter optimization (eps = 0.100000)

[11:44:26] [worker #0] ML tree search #17, logLikelihood: -297303.111746

[11:44:26 -1027870.784212] Initial branch length optimization
[11:44:32 -886545.815548] Model parameter optimization (eps = 10.000000)
[11:45:15 -884948.241086] AUTODETECT spr round 1 (radius: 5)
[11:48:15 -612566.538316] AUTODETECT spr round 2 (radius: 10)
[11:51:49 -462429.231928] AUTODETECT spr round 3 (radius: 15)
[11:56:00 -402096.997365] AUTODETECT spr round 4 (radius: 20)
[12:00:30 -351106.635404] AUTODETECT spr round 5 (radius: 25)
[12:06:28 -341391.114583] SPR radius for FAST iterations: 25 (autodetect)
[12:06:28 -341391.114583] Model parameter optimization (eps = 3.000000)
[12:06:35 -341389.903074] FAST spr round 1 (radius: 25)
[12:10:14 -298929.876603] FAST spr round 2 (radius: 25)
[12:10:38] [worker #1] ML tree search #18, logLikelihood: -297314.870797
[12:12:58 -297657.150119] FAST spr round 3 (radius: 25)
[12:15:24 -297573.040368] FAST spr round 4 (radius: 25)
[12:17:28 -297572.175649] FAST spr round 5 (radius: 25)
[12:19:18 -297572.175643] Model parameter optimization (eps = 1.000000)
[12:19:40 -297452.073383] SLOW spr round 1 (radius: 5)
[12:22:46 -297349.272854] SLOW spr round 2 (radius: 5)
[12:25:46 -297325.753988] SLOW spr round 3 (radius: 5)
[12:28:42 -297320.531748] SLOW spr round 4 (radius: 5)
[12:31:26 -297319.368816] SLOW spr round 5 (radius: 5)
[12:34:04 -297319.362212] SLOW spr round 6 (radius: 10)
[12:36:58 -297316.051789] SLOW spr round 7 (radius: 5)
[12:40:36 -297316.033785] SLOW spr round 8 (radius: 10)
[12:43:38 -297316.033562] SLOW spr round 9 (radius: 15)
[12:48:03 -297316.033483] SLOW spr round 10 (radius: 20)
[12:55:34 -297316.033455] SLOW spr round 11 (radius: 25)
[13:04:40 -297316.033445] Model parameter optimization (eps = 0.100000)

[13:04:49] [worker #0] ML tree search #19, logLikelihood: -297315.741685

[13:29:22] [worker #1] ML tree search #20, logLikelihood: -297313.838529

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.249381,0.229829) (0.313973,0.405068) (0.225789,1.095742) (0.210856,2.694243) 
   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: -297294.411604

AIC score: 598598.823209 / AICc score: 8642658.823209 / BIC score: 607988.961905
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=799).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 40 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.log

Analysis started: 02-Jul-2021 11:09:11 / finished: 03-Jul-2021 00:38:34

Elapsed time: 48563.059 seconds

Consumed energy: 4285.376 Wh (= 21 km in an electric car, or 107 km with an e-scooter!)