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 01-Jul-2021 01:44:50 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/2_msa/Q5SV17_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/3_mltree/Q5SV17 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/2_msa/Q5SV17_trimmed_msa.fasta
[00:00:00] Loaded alignment with 95 taxa and 126 sites

WARNING: Sequences tr_E7FFC9_E7FFC9_DANRE_7955 and tr_W5KYS6_W5KYS6_ASTMX_7994 are exactly identical!
WARNING: Sequences tr_E7FFC9_E7FFC9_DANRE_7955 and tr_W5U970_W5U970_ICTPU_7998 are exactly identical!
WARNING: Sequences sp_B2RWJ3_TM240_MOUSE_10090 and tr_D3ZYD8_D3ZYD8_RAT_10116 are exactly identical!
WARNING: Sequences sp_B2RWJ3_TM240_MOUSE_10090 and tr_A0A1U7QRL8_A0A1U7QRL8_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3QP46_G3QP46_GORGO_9595 and tr_K7DJC9_K7DJC9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QP46_G3QP46_GORGO_9595 and sp_Q5SV17_TM240_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QP46_G3QP46_GORGO_9595 and tr_A0A2R9B9D6_A0A2R9B9D6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J9P8E1_J9P8E1_CANLF_9615 and tr_M3WX45_M3WX45_FELCA_9685 are exactly identical!
WARNING: Sequences tr_J9P8E1_J9P8E1_CANLF_9615 and tr_A0A2U3WFK2_A0A2U3WFK2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_J9P8E1_J9P8E1_CANLF_9615 and tr_A0A2U3XLV9_A0A2U3XLV9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_J9P8E1_J9P8E1_CANLF_9615 and tr_A0A2Y9KAQ7_A0A2Y9KAQ7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M4ADT1_M4ADT1_XIPMA_8083 and tr_I3JRW7_I3JRW7_ORENI_8128 are exactly identical!
WARNING: Sequences tr_M4ADT1_M4ADT1_XIPMA_8083 and tr_G3NMS5_G3NMS5_GASAC_69293 are exactly identical!
WARNING: Sequences tr_M4ADT1_M4ADT1_XIPMA_8083 and tr_A0A087YDA7_A0A087YDA7_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4ADT1_M4ADT1_XIPMA_8083 and tr_A0A2U9BZL5_A0A2U9BZL5_SCOMX_52904 are exactly identical!
WARNING: Sequences tr_A0A1D5QPL0_A0A1D5QPL0_MACMU_9544 and tr_A0A0D9S8X4_A0A0D9S8X4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QPL0_A0A1D5QPL0_MACMU_9544 and tr_A0A2K5MLZ9_A0A2K5MLZ9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QPL0_A0A1D5QPL0_MACMU_9544 and tr_A0A2K6DZD4_A0A2K6DZD4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7CEJ3_F7CEJ3_XENTR_8364 and tr_A0A1L8FM26_A0A1L8FM26_XENLA_8355 are exactly identical!
WARNING: Sequences tr_G3MYY4_G3MYY4_BOVIN_9913 and tr_A0A2U4BXJ6_A0A2U4BXJ6_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G3MYY4_G3MYY4_BOVIN_9913 and tr_A0A2Y9Q9G8_A0A2Y9Q9G8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G3MYY4_G3MYY4_BOVIN_9913 and tr_A0A2Y9SZL3_A0A2Y9SZL3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_R0KFL7_R0KFL7_ANAPL_8839 and tr_A0A091JS40_A0A091JS40_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_R0KFL7_R0KFL7_ANAPL_8839 and tr_A0A091VVR9_A0A091VVR9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_R0KFL7_R0KFL7_ANAPL_8839 and tr_A0A087QS92_A0A087QS92_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A151PIN3_A0A151PIN3_ALLMI_8496 and tr_A0A0Q3LZC0_A0A0Q3LZC0_AMAAE_12930 are exactly identical!
WARNING: Sequences tr_A0A151PIN3_A0A151PIN3_ALLMI_8496 and tr_A0A1U8D5U7_A0A1U8D5U7_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151PIN3_A0A151PIN3_ALLMI_8496 and tr_A0A1V4KNR7_A0A1V4KNR7_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A151PIN3_A0A151PIN3_ALLMI_8496 and tr_A0A226N079_A0A226N079_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A151PIN3_A0A151PIN3_ALLMI_8496 and tr_A0A226PF08_A0A226PF08_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A1S3LBV6_A0A1S3LBV6_SALSA_8030 and tr_A0A060WQB5_A0A060WQB5_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3LIR7_A0A1S3LIR7_SALSA_8030 and tr_A0A060YJ60_A0A060YJ60_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3MDE6_A0A1S3MDE6_SALSA_8030 and tr_A0A060VVV9_A0A060VVV9_ONCMY_8022 are exactly identical!
WARNING: Duplicate sequences found: 33

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/Q5SV17/3_mltree/Q5SV17.raxml.reduced.phy

Alignment comprises 1 partitions and 118 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 126 / 118
Gaps: 3.36 %
Invariant sites: 22.22 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/3_mltree/Q5SV17.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 95 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 118 / 9440
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -7091.687667] Initial branch length optimization
[00:00:00 -5755.664178] Model parameter optimization (eps = 10.000000)
[00:00:02 -5712.446969] AUTODETECT spr round 1 (radius: 5)
[00:00:04 -3466.855905] AUTODETECT spr round 2 (radius: 10)
[00:00:06 -2670.761134] AUTODETECT spr round 3 (radius: 15)
[00:00:08 -2572.942953] AUTODETECT spr round 4 (radius: 20)
[00:00:10 -2572.933304] SPR radius for FAST iterations: 15 (autodetect)
[00:00:10 -2572.933304] Model parameter optimization (eps = 3.000000)
[00:00:20 -2536.347521] FAST spr round 1 (radius: 15)
[00:00:23 -2379.834161] FAST spr round 2 (radius: 15)
[00:00:25 -2344.334238] FAST spr round 3 (radius: 15)
[00:00:26 -2342.355008] FAST spr round 4 (radius: 15)
[00:00:27 -2342.354964] Model parameter optimization (eps = 1.000000)
[00:00:30 -2340.101966] SLOW spr round 1 (radius: 5)
[00:00:33 -2340.101341] SLOW spr round 2 (radius: 10)
[00:00:35 -2340.101337] SLOW spr round 3 (radius: 15)
[00:00:38 -2340.101337] SLOW spr round 4 (radius: 20)
[00:00:41 -2340.101337] SLOW spr round 5 (radius: 25)
[00:00:44 -2340.101337] Model parameter optimization (eps = 0.100000)

[00:00:44] [worker #0] ML tree search #1, logLikelihood: -2340.101318

[00:00:44 -7417.956628] Initial branch length optimization
[00:00:44 -5964.656312] Model parameter optimization (eps = 10.000000)
[00:00:47 -5908.714879] AUTODETECT spr round 1 (radius: 5)
[00:00:48] [worker #1] ML tree search #2, logLikelihood: -2339.460904
[00:00:49 -3312.143351] AUTODETECT spr round 2 (radius: 10)
[00:00:51 -2531.737009] AUTODETECT spr round 3 (radius: 15)
[00:00:53 -2454.237428] AUTODETECT spr round 4 (radius: 20)
[00:00:55 -2454.219110] SPR radius for FAST iterations: 15 (autodetect)
[00:00:55 -2454.219110] Model parameter optimization (eps = 3.000000)
[00:00:58 -2435.468169] FAST spr round 1 (radius: 15)
[00:01:00 -2395.197998] FAST spr round 2 (radius: 15)
[00:01:01 -2371.355011] FAST spr round 3 (radius: 15)
[00:01:03 -2370.158779] FAST spr round 4 (radius: 15)
[00:01:04 -2370.158719] Model parameter optimization (eps = 1.000000)
[00:01:09 -2357.565387] SLOW spr round 1 (radius: 5)
[00:01:12 -2351.970940] SLOW spr round 2 (radius: 5)
[00:01:15 -2351.970838] SLOW spr round 3 (radius: 10)
[00:01:18 -2351.970837] SLOW spr round 4 (radius: 15)
[00:01:21 -2351.970837] SLOW spr round 5 (radius: 20)
[00:01:24 -2351.970837] SLOW spr round 6 (radius: 25)
[00:01:27 -2351.970837] Model parameter optimization (eps = 0.100000)
[00:01:27] [worker #1] ML tree search #4, logLikelihood: -2351.865707

[00:01:28] [worker #0] ML tree search #3, logLikelihood: -2351.866277

[00:01:28 -7128.068839] Initial branch length optimization
[00:01:28 -5818.144615] Model parameter optimization (eps = 10.000000)
[00:01:31 -5774.371003] AUTODETECT spr round 1 (radius: 5)
[00:01:32 -3188.126917] AUTODETECT spr round 2 (radius: 10)
[00:01:34 -2737.494830] AUTODETECT spr round 3 (radius: 15)
[00:01:36 -2608.568833] AUTODETECT spr round 4 (radius: 20)
[00:01:38 -2594.382067] AUTODETECT spr round 5 (radius: 25)
[00:01:40 -2594.381287] SPR radius for FAST iterations: 20 (autodetect)
[00:01:40 -2594.381287] Model parameter optimization (eps = 3.000000)
[00:01:42 -2576.505183] FAST spr round 1 (radius: 20)
[00:01:44 -2395.708272] FAST spr round 2 (radius: 20)
[00:01:45 -2376.903436] FAST spr round 3 (radius: 20)
[00:01:47 -2376.195396] FAST spr round 4 (radius: 20)
[00:01:48 -2376.195394] Model parameter optimization (eps = 1.000000)
[00:01:53 -2359.814353] SLOW spr round 1 (radius: 5)
[00:01:55 -2354.937312] SLOW spr round 2 (radius: 5)
[00:01:58 -2354.937241] SLOW spr round 3 (radius: 10)
[00:02:01 -2354.175995] SLOW spr round 4 (radius: 5)
[00:02:06 -2352.316186] SLOW spr round 5 (radius: 5)
[00:02:09 -2352.316149] SLOW spr round 6 (radius: 10)
[00:02:12 -2352.316145] SLOW spr round 7 (radius: 15)
[00:02:15 -2352.316145] SLOW spr round 8 (radius: 20)
[00:02:18 -2352.316145] SLOW spr round 9 (radius: 25)
[00:02:21 -2352.316145] Model parameter optimization (eps = 0.100000)

[00:02:22] [worker #0] ML tree search #5, logLikelihood: -2351.866119

[00:02:22 -7206.110051] Initial branch length optimization
[00:02:22 -5994.704944] Model parameter optimization (eps = 10.000000)
[00:02:24] [worker #1] ML tree search #6, logLikelihood: -2351.866276
[00:02:25 -5943.998264] AUTODETECT spr round 1 (radius: 5)
[00:02:27 -3477.018515] AUTODETECT spr round 2 (radius: 10)
[00:02:28 -3158.888654] AUTODETECT spr round 3 (radius: 15)
[00:02:31 -2738.345698] AUTODETECT spr round 4 (radius: 20)
[00:02:33 -2701.396788] AUTODETECT spr round 5 (radius: 25)
[00:02:35 -2701.393872] SPR radius for FAST iterations: 20 (autodetect)
[00:02:35 -2701.393872] Model parameter optimization (eps = 3.000000)
[00:02:39 -2677.239918] FAST spr round 1 (radius: 20)
[00:02:41 -2445.351241] FAST spr round 2 (radius: 20)
[00:02:43 -2360.463916] FAST spr round 3 (radius: 20)
[00:02:44 -2358.832867] FAST spr round 4 (radius: 20)
[00:02:46 -2358.832848] Model parameter optimization (eps = 1.000000)
[00:02:48 -2352.394557] SLOW spr round 1 (radius: 5)
[00:02:51 -2352.145024] SLOW spr round 2 (radius: 5)
[00:02:54 -2352.144652] SLOW spr round 3 (radius: 10)
[00:02:56 -2352.144650] SLOW spr round 4 (radius: 15)
[00:02:59 -2352.144650] SLOW spr round 5 (radius: 20)
[00:03:02 -2352.144650] SLOW spr round 6 (radius: 25)
[00:03:05 -2352.144650] Model parameter optimization (eps = 0.100000)
[00:03:06] [worker #1] ML tree search #8, logLikelihood: -2339.503894

[00:03:07] [worker #0] ML tree search #7, logLikelihood: -2351.990397

[00:03:07 -7038.990607] Initial branch length optimization
[00:03:07 -5670.891103] Model parameter optimization (eps = 10.000000)
[00:03:09 -5623.896390] AUTODETECT spr round 1 (radius: 5)
[00:03:10 -3561.861149] AUTODETECT spr round 2 (radius: 10)
[00:03:13 -2681.759911] AUTODETECT spr round 3 (radius: 15)
[00:03:15 -2489.395163] AUTODETECT spr round 4 (radius: 20)
[00:03:17 -2489.363446] SPR radius for FAST iterations: 15 (autodetect)
[00:03:17 -2489.363446] Model parameter optimization (eps = 3.000000)
[00:03:19 -2471.842197] FAST spr round 1 (radius: 15)
[00:03:21 -2403.441696] FAST spr round 2 (radius: 15)
[00:03:23 -2374.451124] FAST spr round 3 (radius: 15)
[00:03:24 -2371.374602] FAST spr round 4 (radius: 15)
[00:03:26 -2371.374507] Model parameter optimization (eps = 1.000000)
[00:03:30 -2353.930299] SLOW spr round 1 (radius: 5)
[00:03:33 -2352.207500] SLOW spr round 2 (radius: 5)
[00:03:35 -2352.207419] SLOW spr round 3 (radius: 10)
[00:03:38 -2351.897409] SLOW spr round 4 (radius: 5)
[00:03:42 -2351.897407] SLOW spr round 5 (radius: 10)
[00:03:45 -2351.897403] SLOW spr round 6 (radius: 15)
[00:03:48 -2351.897403] SLOW spr round 7 (radius: 20)
[00:03:49] [worker #1] ML tree search #10, logLikelihood: -2339.460957
[00:03:51 -2351.897403] SLOW spr round 8 (radius: 25)
[00:03:53 -2351.897403] Model parameter optimization (eps = 0.100000)

[00:03:54] [worker #0] ML tree search #9, logLikelihood: -2351.866724

[00:03:54 -7234.011449] Initial branch length optimization
[00:03:54 -5807.043671] Model parameter optimization (eps = 10.000000)
[00:03:57 -5757.115155] AUTODETECT spr round 1 (radius: 5)
[00:03:59 -3400.439893] AUTODETECT spr round 2 (radius: 10)
[00:04:01 -2800.050588] AUTODETECT spr round 3 (radius: 15)
[00:04:03 -2610.989796] AUTODETECT spr round 4 (radius: 20)
[00:04:05 -2610.644914] AUTODETECT spr round 5 (radius: 25)
[00:04:06 -2610.644866] SPR radius for FAST iterations: 20 (autodetect)
[00:04:06 -2610.644866] Model parameter optimization (eps = 3.000000)
[00:04:11 -2592.193751] FAST spr round 1 (radius: 20)
[00:04:13 -2383.412004] FAST spr round 2 (radius: 20)
[00:04:15 -2371.066374] FAST spr round 3 (radius: 20)
[00:04:16 -2371.065625] Model parameter optimization (eps = 1.000000)
[00:04:21 -2356.187835] SLOW spr round 1 (radius: 5)
[00:04:24 -2352.529360] SLOW spr round 2 (radius: 5)
[00:04:27 -2352.529300] SLOW spr round 3 (radius: 10)
[00:04:29 -2352.529297] SLOW spr round 4 (radius: 15)
[00:04:31] [worker #1] ML tree search #12, logLikelihood: -2339.503881
[00:04:33 -2352.226024] SLOW spr round 5 (radius: 5)
[00:04:37 -2352.226023] SLOW spr round 6 (radius: 10)
[00:04:40 -2352.226023] SLOW spr round 7 (radius: 15)
[00:04:43 -2352.226023] SLOW spr round 8 (radius: 20)
[00:04:45 -2352.226023] SLOW spr round 9 (radius: 25)
[00:04:48 -2352.226023] Model parameter optimization (eps = 0.100000)

[00:04:50] [worker #0] ML tree search #11, logLikelihood: -2351.866615

[00:04:50 -7290.823100] Initial branch length optimization
[00:04:50 -5910.533126] Model parameter optimization (eps = 10.000000)
[00:04:53 -5859.247375] AUTODETECT spr round 1 (radius: 5)
[00:04:54 -3593.351602] AUTODETECT spr round 2 (radius: 10)
[00:04:56 -2648.954455] AUTODETECT spr round 3 (radius: 15)
[00:04:59 -2534.015797] AUTODETECT spr round 4 (radius: 20)
[00:05:01 -2533.967862] SPR radius for FAST iterations: 15 (autodetect)
[00:05:01 -2533.967862] Model parameter optimization (eps = 3.000000)
[00:05:04 -2522.377400] FAST spr round 1 (radius: 15)
[00:05:06 -2410.394641] FAST spr round 2 (radius: 15)
[00:05:08 -2376.671399] FAST spr round 3 (radius: 15)
[00:05:09 -2375.655046] FAST spr round 4 (radius: 15)
[00:05:10 -2375.654945] Model parameter optimization (eps = 1.000000)
[00:05:13] [worker #1] ML tree search #14, logLikelihood: -2353.324709
[00:05:17 -2357.771448] SLOW spr round 1 (radius: 5)
[00:05:20 -2352.288905] SLOW spr round 2 (radius: 5)
[00:05:23 -2352.288692] SLOW spr round 3 (radius: 10)
[00:05:25 -2351.970681] SLOW spr round 4 (radius: 5)
[00:05:29 -2351.970672] SLOW spr round 5 (radius: 10)
[00:05:33 -2351.970672] SLOW spr round 6 (radius: 15)
[00:05:35 -2351.970672] SLOW spr round 7 (radius: 20)
[00:05:39 -2351.970672] SLOW spr round 8 (radius: 25)
[00:05:41 -2351.970672] Model parameter optimization (eps = 0.100000)

[00:05:42] [worker #0] ML tree search #13, logLikelihood: -2351.866291

[00:05:42 -6921.535705] Initial branch length optimization
[00:05:42 -5649.053196] Model parameter optimization (eps = 10.000000)
[00:05:46 -5586.035772] AUTODETECT spr round 1 (radius: 5)
[00:05:47 -3416.956161] AUTODETECT spr round 2 (radius: 10)
[00:05:49 -2912.579012] AUTODETECT spr round 3 (radius: 15)
[00:05:52 -2501.673627] AUTODETECT spr round 4 (radius: 20)
[00:05:54 -2501.658275] SPR radius for FAST iterations: 15 (autodetect)
[00:05:54 -2501.658275] Model parameter optimization (eps = 3.000000)
[00:05:56] [worker #1] ML tree search #16, logLikelihood: -2340.101196
[00:06:00 -2459.523270] FAST spr round 1 (radius: 15)
[00:06:01 -2369.537625] FAST spr round 2 (radius: 15)
[00:06:03 -2343.537773] FAST spr round 3 (radius: 15)
[00:06:05 -2340.235212] FAST spr round 4 (radius: 15)
[00:06:06 -2340.181356] Model parameter optimization (eps = 1.000000)
[00:06:07 -2339.507177] SLOW spr round 1 (radius: 5)
[00:06:10 -2339.494217] SLOW spr round 2 (radius: 10)
[00:06:13 -2339.494154] SLOW spr round 3 (radius: 15)
[00:06:16 -2339.494152] SLOW spr round 4 (radius: 20)
[00:06:19 -2339.494152] SLOW spr round 5 (radius: 25)
[00:06:22 -2339.494152] Model parameter optimization (eps = 0.100000)

[00:06:22] [worker #0] ML tree search #15, logLikelihood: -2339.460900

[00:06:22 -7271.915149] Initial branch length optimization
[00:06:23 -5893.538092] Model parameter optimization (eps = 10.000000)
[00:06:25 -5853.394402] AUTODETECT spr round 1 (radius: 5)
[00:06:27 -3319.457266] AUTODETECT spr round 2 (radius: 10)
[00:06:29 -2603.130334] AUTODETECT spr round 3 (radius: 15)
[00:06:31 -2578.257208] AUTODETECT spr round 4 (radius: 20)
[00:06:33 -2569.364636] AUTODETECT spr round 5 (radius: 25)
[00:06:35 -2569.313332] SPR radius for FAST iterations: 20 (autodetect)
[00:06:35 -2569.313332] Model parameter optimization (eps = 3.000000)
[00:06:42 -2528.303279] FAST spr round 1 (radius: 20)
[00:06:43] [worker #1] ML tree search #18, logLikelihood: -2339.461842
[00:06:44 -2362.825923] FAST spr round 2 (radius: 20)
[00:06:46 -2347.447277] FAST spr round 3 (radius: 20)
[00:06:47 -2346.105552] FAST spr round 4 (radius: 20)
[00:06:48 -2346.105453] Model parameter optimization (eps = 1.000000)
[00:06:51 -2340.102804] SLOW spr round 1 (radius: 5)
[00:06:54 -2340.101479] SLOW spr round 2 (radius: 10)
[00:06:56 -2340.101456] SLOW spr round 3 (radius: 15)
[00:06:59 -2340.101455] SLOW spr round 4 (radius: 20)
[00:07:01 -2340.101455] SLOW spr round 5 (radius: 25)
[00:07:04 -2340.101455] Model parameter optimization (eps = 0.100000)

[00:07:04] [worker #0] ML tree search #17, logLikelihood: -2340.101350

[00:07:04 -6928.842553] Initial branch length optimization
[00:07:05 -5763.284308] Model parameter optimization (eps = 10.000000)
[00:07:07 -5716.350598] AUTODETECT spr round 1 (radius: 5)
[00:07:08 -3218.994320] AUTODETECT spr round 2 (radius: 10)
[00:07:10 -2632.179007] AUTODETECT spr round 3 (radius: 15)
[00:07:13 -2482.306562] AUTODETECT spr round 4 (radius: 20)
[00:07:15 -2482.280974] SPR radius for FAST iterations: 15 (autodetect)
[00:07:15 -2482.280974] Model parameter optimization (eps = 3.000000)
[00:07:20 -2453.682509] FAST spr round 1 (radius: 15)
[00:07:23 -2366.719016] FAST spr round 2 (radius: 15)
[00:07:24 -2353.649057] FAST spr round 3 (radius: 15)
[00:07:26 -2351.966462] FAST spr round 4 (radius: 15)
[00:07:27 -2351.966459] Model parameter optimization (eps = 1.000000)
[00:07:30] [worker #1] ML tree search #20, logLikelihood: -2351.866220
[00:07:31 -2343.742095] SLOW spr round 1 (radius: 5)
[00:07:34 -2341.746265] SLOW spr round 2 (radius: 5)
[00:07:37 -2341.746186] SLOW spr round 3 (radius: 10)
[00:07:39 -2341.746186] SLOW spr round 4 (radius: 15)
[00:07:42 -2341.746186] SLOW spr round 5 (radius: 20)
[00:07:45 -2341.746186] SLOW spr round 6 (radius: 25)
[00:07:47 -2341.746186] Model parameter optimization (eps = 0.100000)

[00:07:49] [worker #0] ML tree search #19, logLikelihood: -2341.661200


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.168859,1.305381) (0.128368,4.038450) (0.594275,0.199594) (0.108498,1.313892) 
   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: -2339.460900

AIC score: 5064.921799 / AICc score: 79948.921799 / BIC score: 5612.324207
Free parameters (model + branch lengths): 193

WARNING: Number of free parameters (K=193) is larger than alignment size (n=126).
         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/Q5SV17/3_mltree/Q5SV17.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/3_mltree/Q5SV17.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/3_mltree/Q5SV17.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SV17/3_mltree/Q5SV17.raxml.log

Analysis started: 01-Jul-2021 01:44:50 / finished: 01-Jul-2021 01:52:40

Elapsed time: 469.096 seconds

Consumed energy: 37.171 Wh