RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 12-Jul-2021 08:19:08 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/2_msa/Q9H7M6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6 --seed 2 --threads 8 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/2_msa/Q9H7M6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 562 taxa and 791 sites

WARNING: Sequences tr_G3QTN3_G3QTN3_GORGO_9595 and sp_A7E2V4_ZSWM8_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29HK6_Q29HK6_DROPS_46245 and tr_B4GXJ0_B4GXJ0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2PYW9_H2PYW9_PANTR_9598 and sp_Q9P217_ZSWM5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QQY6_H2QQY6_PANTR_9598 and tr_A0A2R9CEN6_A0A2R9CEN6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0G2K9R0_A0A0G2K9R0_RAT_10116 and tr_D4A5A9_D4A5A9_RAT_10116 are exactly identical!
WARNING: Sequences tr_M4AME6_M4AME6_XIPMA_8083 and tr_I3KD20_I3KD20_ORENI_8128 are exactly identical!
WARNING: Sequences tr_M4AME6_M4AME6_XIPMA_8083 and tr_A0A087YMW9_A0A087YMW9_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088ADL5_A0A088ADL5_APIME_7460 and tr_A0A2A3EPB1_A0A2A3EPB1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NYL8_A0A158NYL8_ATTCE_12957 and tr_F4WXZ4_F4WXZ4_ACREC_103372 are exactly identical!
WARNING: Sequences tr_I3N273_I3N273_ICTTR_43179 and tr_M3WNW2_M3WNW2_FELCA_9685 are exactly identical!
WARNING: Sequences tr_I3N273_I3N273_ICTTR_43179 and tr_A0A384CI33_A0A384CI33_URSMA_29073 are exactly identical!
WARNING: Sequences tr_H0X1M3_H0X1M3_OTOGA_30611 and tr_G1LC38_G1LC38_AILME_9646 are exactly identical!
WARNING: Sequences tr_H2UFK2_H2UFK2_TAKRU_31033 and tr_H3DJP9_H3DJP9_TETNG_99883 are exactly identical!
WARNING: Sequences tr_F6Q8J2_F6Q8J2_MACMU_9544 and tr_A0A2K5L0L3_A0A2K5L0L3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6Q8J2_F6Q8J2_MACMU_9544 and tr_A0A2K6DY87_A0A2K6DY87_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6Q8J2_F6Q8J2_MACMU_9544 and tr_A0A2K5ZKR3_A0A2K5ZKR3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6UIJ2_F6UIJ2_MACMU_9544 and tr_G7PZK1_G7PZK1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6UIJ2_F6UIJ2_MACMU_9544 and tr_A0A0A0MW84_A0A0A0MW84_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HBW5_F7HBW5_MACMU_9544 and tr_A0A0D9RU16_A0A0D9RU16_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7HR44_F7HR44_MACMU_9544 and tr_A0A2K5N853_A0A2K5N853_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HR44_F7HR44_MACMU_9544 and tr_A0A2K6DMB7_A0A2K6DMB7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HR44_F7HR44_MACMU_9544 and tr_A0A2K5ZPI1_A0A2K5ZPI1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z971_H0Z971_TAEGU_59729 and tr_A0A218UW52_A0A218UW52_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_U3IQQ9_U3IQQ9_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A091VAY5_A0A091VAY5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A087RHK4_A0A087RHK4_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A091GKT5_A0A091GKT5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A2I0LYW6_A0A2I0LYW6_COLLI_8932 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A093GNY6_A0A093GNY6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A091HTS2_A0A091HTS2_CALAN_9244 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A1V4JX11_A0A1V4JX11_PATFA_372326 are exactly identical!
WARNING: Sequences tr_H0ZC08_H0ZC08_TAEGU_59729 and tr_A0A226NLV7_A0A226NLV7_CALSU_9009 are exactly identical!
WARNING: Sequences tr_G7P7L1_G7P7L1_MACFA_9541 and tr_A0A2I3N0U7_A0A2I3N0U7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7P7L1_G7P7L1_MACFA_9541 and tr_A0A2K5LC12_A0A2K5LC12_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151MSW3_A0A151MSW3_ALLMI_8496 and tr_A0A1U8DFB8_A0A1U8DFB8_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V0WZB1_A0A0V0WZB1_9BILA_92179 and tr_A0A0V1L9N7_A0A0V1L9N7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1MV75_A0A0V1MV75_9BILA_268474 and tr_A0A0V1I4L3_A0A0V1I4L3_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A226NH17_A0A226NH17_CALSU_9009 and tr_A0A226PCD7_A0A226PCD7_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QMV5_A0A2D0QMV5_ICTPU_7998 and tr_A0A2D0QNM3_A0A2D0QNM3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4AX63_A0A2U4AX63_TURTR_9739 and tr_A0A2U3ZXR4_A0A2U3ZXR4_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A2U4AX63_A0A2U4AX63_TURTR_9739 and tr_A0A2U3YQE8_A0A2U3YQE8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U4BK59_A0A2U4BK59_TURTR_9739 and tr_A0A383YPN3_A0A383YPN3_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 42

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.reduced.phy

Alignment comprises 1 partitions and 791 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 791 / 791
Gaps: 16.13 %
Invariant sites: 0.13 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.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 562 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 198 / 15840
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -574741.306583] Initial branch length optimization
[00:00:03 -421939.520873] Model parameter optimization (eps = 10.000000)
[00:00:30 -421301.323018] AUTODETECT spr round 1 (radius: 5)
[00:01:30 -236685.821110] AUTODETECT spr round 2 (radius: 10)
[00:02:36 -165668.891667] AUTODETECT spr round 3 (radius: 15)
[00:04:01 -123177.099899] AUTODETECT spr round 4 (radius: 20)
[00:05:30 -114015.645815] AUTODETECT spr round 5 (radius: 25)
[00:07:11 -112573.550246] SPR radius for FAST iterations: 25 (autodetect)
[00:07:11 -112573.550246] Model parameter optimization (eps = 3.000000)
[00:07:41 -112067.632226] FAST spr round 1 (radius: 25)
[00:09:08 -99720.825545] FAST spr round 2 (radius: 25)
[00:10:13 -99209.675160] FAST spr round 3 (radius: 25)
[00:11:11 -99189.194463] FAST spr round 4 (radius: 25)
[00:12:02 -99112.703411] FAST spr round 5 (radius: 25)
[00:12:50 -99111.070683] FAST spr round 6 (radius: 25)
[00:13:36 -99111.070496] Model parameter optimization (eps = 1.000000)
[00:13:54 -99097.518724] SLOW spr round 1 (radius: 5)
[00:15:03 -99089.230143] SLOW spr round 2 (radius: 5)
[00:16:09 -99088.547078] SLOW spr round 3 (radius: 5)
[00:17:14 -99088.545019] SLOW spr round 4 (radius: 10)
[00:18:27 -99087.857339] SLOW spr round 5 (radius: 5)
[00:19:53 -99087.822585] SLOW spr round 6 (radius: 10)
[00:21:22 -99087.822530] SLOW spr round 7 (radius: 15)
[00:23:08 -99084.985466] SLOW spr round 8 (radius: 5)
[00:24:37 -99084.985179] SLOW spr round 9 (radius: 10)
[00:26:09 -99084.985076] SLOW spr round 10 (radius: 15)
[00:27:54 -99084.985036] SLOW spr round 11 (radius: 20)
[00:30:26 -99084.985016] SLOW spr round 12 (radius: 25)
[00:30:27] [worker #1] ML tree search #2, logLikelihood: -99089.313741
[00:33:22 -99084.985004] Model parameter optimization (eps = 0.100000)

[00:33:26] [worker #0] ML tree search #1, logLikelihood: -99084.965557

[00:33:26 -573444.352021] Initial branch length optimization
[00:33:31 -423752.522107] Model parameter optimization (eps = 10.000000)
[00:33:59 -422976.671157] AUTODETECT spr round 1 (radius: 5)
[00:34:58 -236012.953571] AUTODETECT spr round 2 (radius: 10)
[00:36:06 -162686.447970] AUTODETECT spr round 3 (radius: 15)
[00:37:22 -136887.146775] AUTODETECT spr round 4 (radius: 20)
[00:38:53 -119045.174859] AUTODETECT spr round 5 (radius: 25)
[00:40:32 -114100.731621] SPR radius for FAST iterations: 25 (autodetect)
[00:40:32 -114100.731621] Model parameter optimization (eps = 3.000000)
[00:40:57 -113616.862902] FAST spr round 1 (radius: 25)
[00:42:24 -100945.239872] FAST spr round 2 (radius: 25)
[00:43:33 -99115.768150] FAST spr round 3 (radius: 25)
[00:44:28 -99111.320020] FAST spr round 4 (radius: 25)
[00:45:17 -99111.147549] FAST spr round 5 (radius: 25)
[00:46:03 -99111.138683] Model parameter optimization (eps = 1.000000)
[00:46:18 -99104.549841] SLOW spr round 1 (radius: 5)
[00:47:26 -99091.617702] SLOW spr round 2 (radius: 5)
[00:48:33 -99088.783788] SLOW spr round 3 (radius: 5)
[00:49:37 -99088.781840] SLOW spr round 4 (radius: 10)
[00:50:49 -99088.112263] SLOW spr round 5 (radius: 5)
[00:52:13 -99088.090024] SLOW spr round 6 (radius: 10)
[00:53:41 -99087.582075] SLOW spr round 7 (radius: 5)
[00:55:03 -99087.581052] SLOW spr round 8 (radius: 10)
[00:56:27 -99087.580318] SLOW spr round 9 (radius: 15)
[00:58:14 -99087.579716] SLOW spr round 10 (radius: 20)
[00:58:29] [worker #1] ML tree search #4, logLikelihood: -99079.232569
[01:00:48 -99087.579235] SLOW spr round 11 (radius: 25)
[01:03:45 -99087.578842] Model parameter optimization (eps = 0.100000)

[01:03:53] [worker #0] ML tree search #3, logLikelihood: -99087.460108

[01:03:54 -554554.291098] Initial branch length optimization
[01:03:56 -411559.409581] Model parameter optimization (eps = 10.000000)
[01:04:20 -410772.474982] AUTODETECT spr round 1 (radius: 5)
[01:05:18 -232363.705481] AUTODETECT spr round 2 (radius: 10)
[01:06:24 -154606.753675] AUTODETECT spr round 3 (radius: 15)
[01:07:36 -125763.853398] AUTODETECT spr round 4 (radius: 20)
[01:08:56 -121460.612642] AUTODETECT spr round 5 (radius: 25)
[01:10:31 -114501.921011] SPR radius for FAST iterations: 25 (autodetect)
[01:10:31 -114501.921011] Model parameter optimization (eps = 3.000000)
[01:10:59 -114116.475076] FAST spr round 1 (radius: 25)
[01:12:23 -99877.812206] FAST spr round 2 (radius: 25)
[01:13:27 -99156.917563] FAST spr round 3 (radius: 25)
[01:14:24 -99137.759823] FAST spr round 4 (radius: 25)
[01:15:12 -99137.575663] FAST spr round 5 (radius: 25)
[01:15:58 -99137.512494] Model parameter optimization (eps = 1.000000)
[01:16:15 -99112.748584] SLOW spr round 1 (radius: 5)
[01:17:21 -99106.122905] SLOW spr round 2 (radius: 5)
[01:18:30 -99105.913866] SLOW spr round 3 (radius: 5)
[01:19:36 -99105.892328] SLOW spr round 4 (radius: 10)
[01:20:49 -99096.837250] SLOW spr round 5 (radius: 5)
[01:22:13 -99096.832901] SLOW spr round 6 (radius: 10)
[01:23:39 -99096.832253] SLOW spr round 7 (radius: 15)
[01:25:24 -99095.474126] SLOW spr round 8 (radius: 5)
[01:26:53 -99095.393112] SLOW spr round 9 (radius: 10)
[01:28:24 -99091.599149] SLOW spr round 10 (radius: 5)
[01:29:46 -99091.598423] SLOW spr round 11 (radius: 10)
[01:31:08 -99091.597090] SLOW spr round 12 (radius: 15)
[01:32:51 -99091.596661] SLOW spr round 13 (radius: 20)
[01:35:21 -99091.596326] SLOW spr round 14 (radius: 25)
[01:38:20 -99091.596065] Model parameter optimization (eps = 0.100000)

[01:38:26] [worker #0] ML tree search #5, logLikelihood: -99091.502297

[01:38:26 -557479.761998] Initial branch length optimization
[01:38:29 -419627.512287] Model parameter optimization (eps = 10.000000)
[01:38:55 -418935.206746] AUTODETECT spr round 1 (radius: 5)
[01:39:54 -233199.047378] AUTODETECT spr round 2 (radius: 10)
[01:40:57 -168334.105144] AUTODETECT spr round 3 (radius: 15)
[01:41:56] [worker #1] ML tree search #6, logLikelihood: -99142.634564
[01:42:13 -137030.029717] AUTODETECT spr round 4 (radius: 20)
[01:43:40 -123839.304251] AUTODETECT spr round 5 (radius: 25)
[01:45:19 -123270.221159] SPR radius for FAST iterations: 25 (autodetect)
[01:45:19 -123270.221159] Model parameter optimization (eps = 3.000000)
[01:45:41 -122959.583878] FAST spr round 1 (radius: 25)
[01:47:05 -102989.476136] FAST spr round 2 (radius: 25)
[01:48:14 -99945.624684] FAST spr round 3 (radius: 25)
[01:49:13 -99334.712177] FAST spr round 4 (radius: 25)
[01:50:06 -99217.131861] FAST spr round 5 (radius: 25)
[01:50:54 -99213.315907] FAST spr round 6 (radius: 25)
[01:51:39 -99213.315192] Model parameter optimization (eps = 1.000000)
[01:51:59 -99177.164374] SLOW spr round 1 (radius: 5)
[01:53:07 -99134.857876] SLOW spr round 2 (radius: 5)
[01:54:16 -99130.512473] SLOW spr round 3 (radius: 5)
[01:55:26 -99130.431172] SLOW spr round 4 (radius: 10)
[01:56:42 -99130.039648] SLOW spr round 5 (radius: 5)
[01:58:10 -99130.039540] SLOW spr round 6 (radius: 10)
[01:59:39 -99130.039531] SLOW spr round 7 (radius: 15)
[02:01:25 -99130.039526] SLOW spr round 8 (radius: 20)
[02:04:01 -99130.039522] SLOW spr round 9 (radius: 25)
[02:06:59 -99090.287834] SLOW spr round 10 (radius: 5)
[02:08:33 -99090.286850] SLOW spr round 11 (radius: 10)
[02:08:48] [worker #1] ML tree search #8, logLikelihood: -99144.731531
[02:10:10 -99090.280562] SLOW spr round 12 (radius: 15)
[02:11:54 -99090.280528] SLOW spr round 13 (radius: 20)
[02:14:35 -99089.451860] SLOW spr round 14 (radius: 5)
[02:16:12 -99089.028359] SLOW spr round 15 (radius: 5)
[02:17:35 -99089.013383] SLOW spr round 16 (radius: 10)
[02:18:59 -99088.768365] SLOW spr round 17 (radius: 5)
[02:20:25 -99088.767409] SLOW spr round 18 (radius: 10)
[02:21:51 -99088.767306] SLOW spr round 19 (radius: 15)
[02:23:36 -99088.767289] SLOW spr round 20 (radius: 20)
[02:26:11 -99088.767283] SLOW spr round 21 (radius: 25)
[02:29:12 -99088.767278] Model parameter optimization (eps = 0.100000)

[02:29:22] [worker #0] ML tree search #7, logLikelihood: -99088.288193

[02:29:22 -568708.817255] Initial branch length optimization
[02:29:26 -416422.482083] Model parameter optimization (eps = 10.000000)
[02:29:58 -415684.381372] AUTODETECT spr round 1 (radius: 5)
[02:31:01 -234660.339229] AUTODETECT spr round 2 (radius: 10)
[02:32:09 -175818.074766] AUTODETECT spr round 3 (radius: 15)
[02:33:33 -135444.652051] AUTODETECT spr round 4 (radius: 20)
[02:35:06 -120884.331461] AUTODETECT spr round 5 (radius: 25)
[02:37:01 -113662.895583] SPR radius for FAST iterations: 25 (autodetect)
[02:37:01 -113662.895583] Model parameter optimization (eps = 3.000000)
[02:37:34 -113158.538491] FAST spr round 1 (radius: 25)
[02:38:57 -99577.548337] FAST spr round 2 (radius: 25)
[02:40:01 -99220.701753] FAST spr round 3 (radius: 25)
[02:40:56 -99188.571587] FAST spr round 4 (radius: 25)
[02:41:44 -99188.567387] Model parameter optimization (eps = 1.000000)
[02:41:58 -99180.037762] SLOW spr round 1 (radius: 5)
[02:43:10 -99154.558335] SLOW spr round 2 (radius: 5)
[02:44:20 -99153.451783] SLOW spr round 3 (radius: 5)
[02:45:29 -99153.331739] SLOW spr round 4 (radius: 5)
[02:46:36 -99153.312216] SLOW spr round 5 (radius: 10)
[02:47:48] [worker #1] ML tree search #10, logLikelihood: -99080.142266
[02:47:49 -99151.511940] SLOW spr round 6 (radius: 5)
[02:49:18 -99151.316375] SLOW spr round 7 (radius: 5)
[02:50:37 -99151.316226] SLOW spr round 8 (radius: 10)
[02:51:56 -99151.302774] SLOW spr round 9 (radius: 15)
[02:53:44 -99150.339846] SLOW spr round 10 (radius: 5)
[02:55:18 -99148.394838] SLOW spr round 11 (radius: 5)
[02:56:38 -99146.844698] SLOW spr round 12 (radius: 5)
[02:57:50 -99146.844265] SLOW spr round 13 (radius: 10)
[02:59:05 -99146.844247] SLOW spr round 14 (radius: 15)
[03:00:54 -99146.844236] SLOW spr round 15 (radius: 20)
[03:03:21 -99146.844228] SLOW spr round 16 (radius: 25)
[03:06:16 -99146.844221] Model parameter optimization (eps = 0.100000)

[03:06:26] [worker #0] ML tree search #9, logLikelihood: -99146.526629

[03:06:26 -564736.811705] Initial branch length optimization
[03:06:29 -418492.990257] Model parameter optimization (eps = 10.000000)
[03:07:02 -417822.025359] AUTODETECT spr round 1 (radius: 5)
[03:08:03 -234960.813101] AUTODETECT spr round 2 (radius: 10)
[03:09:10 -165643.129587] AUTODETECT spr round 3 (radius: 15)
[03:10:23 -131357.022483] AUTODETECT spr round 4 (radius: 20)
[03:11:52 -111927.553841] AUTODETECT spr round 5 (radius: 25)
[03:13:32 -111212.381647] SPR radius for FAST iterations: 25 (autodetect)
[03:13:32 -111212.381647] Model parameter optimization (eps = 3.000000)
[03:14:00 -110724.570049] FAST spr round 1 (radius: 25)
[03:15:05] [worker #1] ML tree search #12, logLikelihood: -99078.428843
[03:15:26 -99424.661429] FAST spr round 2 (radius: 25)
[03:16:42 -99160.421882] FAST spr round 3 (radius: 25)
[03:17:38 -99128.042617] FAST spr round 4 (radius: 25)
[03:18:29 -99127.649992] FAST spr round 5 (radius: 25)
[03:19:18 -99127.647580] Model parameter optimization (eps = 1.000000)
[03:19:39 -99117.087817] SLOW spr round 1 (radius: 5)
[03:20:49 -99101.753176] SLOW spr round 2 (radius: 5)
[03:22:01 -99098.401519] SLOW spr round 3 (radius: 5)
[03:23:11 -99098.400611] SLOW spr round 4 (radius: 10)
[03:24:26 -99095.554194] SLOW spr round 5 (radius: 5)
[03:25:54 -99095.553682] SLOW spr round 6 (radius: 10)
[03:27:22 -99095.446391] SLOW spr round 7 (radius: 5)
[03:28:46 -99095.446341] SLOW spr round 8 (radius: 10)
[03:30:11 -99095.446266] SLOW spr round 9 (radius: 15)
[03:32:00 -99095.446252] SLOW spr round 10 (radius: 20)
[03:34:39 -99095.446240] SLOW spr round 11 (radius: 25)
[03:37:44 -99095.446228] Model parameter optimization (eps = 0.100000)

[03:37:56] [worker #0] ML tree search #11, logLikelihood: -99095.136272

[03:37:56 -578541.093602] Initial branch length optimization
[03:38:00 -423341.813763] Model parameter optimization (eps = 10.000000)
[03:38:29 -422491.007972] AUTODETECT spr round 1 (radius: 5)
[03:39:32 -241676.338205] AUTODETECT spr round 2 (radius: 10)
[03:40:39 -169445.908260] AUTODETECT spr round 3 (radius: 15)
[03:41:59 -125392.573633] AUTODETECT spr round 4 (radius: 20)
[03:43:36 -111643.703046] AUTODETECT spr round 5 (radius: 25)
[03:45:33 -110249.160871] SPR radius for FAST iterations: 25 (autodetect)
[03:45:33 -110249.160871] Model parameter optimization (eps = 3.000000)
[03:46:07 -109824.689847] FAST spr round 1 (radius: 25)
[03:47:24 -99462.037483] FAST spr round 2 (radius: 25)
[03:48:36 -99198.477583] FAST spr round 3 (radius: 25)
[03:49:33 -99123.096933] FAST spr round 4 (radius: 25)
[03:50:24 -99120.254029] FAST spr round 5 (radius: 25)
[03:51:12 -99120.251776] Model parameter optimization (eps = 1.000000)
[03:51:22 -99114.470520] SLOW spr round 1 (radius: 5)
[03:52:31 -99090.298595] SLOW spr round 2 (radius: 5)
[03:53:40 -99090.230672] SLOW spr round 3 (radius: 10)
[03:54:52 -99089.908359] SLOW spr round 4 (radius: 5)
[03:55:04] [worker #1] ML tree search #14, logLikelihood: -99083.217330
[03:56:23 -99089.887427] SLOW spr round 5 (radius: 10)
[03:57:53 -99089.887104] SLOW spr round 6 (radius: 15)
[03:59:43 -99089.886885] SLOW spr round 7 (radius: 20)
[04:02:16 -99089.447315] SLOW spr round 8 (radius: 5)
[04:03:51 -99089.444761] SLOW spr round 9 (radius: 10)
[04:05:25 -99089.443135] SLOW spr round 10 (radius: 15)
[04:07:16 -99089.441868] SLOW spr round 11 (radius: 20)
[04:09:52 -99089.440877] SLOW spr round 12 (radius: 25)
[04:12:52 -99089.440098] Model parameter optimization (eps = 0.100000)

[04:12:58] [worker #0] ML tree search #13, logLikelihood: -99089.404353

[04:12:58 -567758.431576] Initial branch length optimization
[04:13:01 -422995.462271] Model parameter optimization (eps = 10.000000)
[04:13:34 -422288.323632] AUTODETECT spr round 1 (radius: 5)
[04:14:34 -239966.765362] AUTODETECT spr round 2 (radius: 10)
[04:15:42 -171456.845991] AUTODETECT spr round 3 (radius: 15)
[04:17:00 -129035.686255] AUTODETECT spr round 4 (radius: 20)
[04:18:28 -117804.766706] AUTODETECT spr round 5 (radius: 25)
[04:20:08 -113064.206488] SPR radius for FAST iterations: 25 (autodetect)
[04:20:08 -113064.206488] Model parameter optimization (eps = 3.000000)
[04:20:37 -112593.073836] FAST spr round 1 (radius: 25)
[04:21:59 -99883.988781] FAST spr round 2 (radius: 25)
[04:23:06 -99142.333174] FAST spr round 3 (radius: 25)
[04:23:09] [worker #1] ML tree search #16, logLikelihood: -99091.360822
[04:24:06 -99119.643025] FAST spr round 4 (radius: 25)
[04:25:00 -99113.612922] FAST spr round 5 (radius: 25)
[04:25:50 -99111.388853] FAST spr round 6 (radius: 25)
[04:26:39 -99111.387947] Model parameter optimization (eps = 1.000000)
[04:27:02 -99096.422996] SLOW spr round 1 (radius: 5)
[04:28:12 -99086.977941] SLOW spr round 2 (radius: 5)
[04:29:24 -99085.891026] SLOW spr round 3 (radius: 5)
[04:30:33 -99085.889203] SLOW spr round 4 (radius: 10)
[04:31:46 -99085.888846] SLOW spr round 5 (radius: 15)
[04:33:39 -99085.888699] SLOW spr round 6 (radius: 20)
[04:36:10 -99085.888617] SLOW spr round 7 (radius: 25)
[04:39:14 -99085.888563] Model parameter optimization (eps = 0.100000)

[04:39:25] [worker #0] ML tree search #15, logLikelihood: -99085.688028

[04:39:25 -575703.767195] Initial branch length optimization
[04:39:29 -423422.799601] Model parameter optimization (eps = 10.000000)
[04:40:01 -422661.103016] AUTODETECT spr round 1 (radius: 5)
[04:41:04 -230589.141028] AUTODETECT spr round 2 (radius: 10)
[04:42:13 -162369.609678] AUTODETECT spr round 3 (radius: 15)
[04:43:37 -129780.060894] AUTODETECT spr round 4 (radius: 20)
[04:45:02 -110440.706707] AUTODETECT spr round 5 (radius: 25)
[04:46:38 -109162.110798] SPR radius for FAST iterations: 25 (autodetect)
[04:46:38 -109162.110798] Model parameter optimization (eps = 3.000000)
[04:47:08 -108678.183152] FAST spr round 1 (radius: 25)
[04:48:27 -99580.386169] FAST spr round 2 (radius: 25)
[04:49:31 -99153.901080] FAST spr round 3 (radius: 25)
[04:50:27 -99141.319247] FAST spr round 4 (radius: 25)
[04:51:18 -99135.604078] FAST spr round 5 (radius: 25)
[04:52:06 -99135.604048] Model parameter optimization (eps = 1.000000)
[04:52:24 -99123.456195] SLOW spr round 1 (radius: 5)
[04:53:32 -99098.448094] SLOW spr round 2 (radius: 5)
[04:54:42 -99096.525602] SLOW spr round 3 (radius: 5)
[04:55:53 -99092.060462] SLOW spr round 4 (radius: 5)
[04:57:02 -99092.058130] SLOW spr round 5 (radius: 10)
[04:58:17 -99084.055300] SLOW spr round 6 (radius: 5)
[04:59:45 -99083.997395] SLOW spr round 7 (radius: 10)
[05:01:05] [worker #1] ML tree search #18, logLikelihood: -99086.532695
[05:01:16 -99083.995739] SLOW spr round 8 (radius: 15)
[05:03:06 -99083.755485] SLOW spr round 9 (radius: 5)
[05:04:39 -99083.754937] SLOW spr round 10 (radius: 10)
[05:06:11 -99083.754787] SLOW spr round 11 (radius: 15)
[05:07:58 -99083.754729] SLOW spr round 12 (radius: 20)
[05:10:28 -99083.754706] SLOW spr round 13 (radius: 25)
[05:13:33 -99083.754696] Model parameter optimization (eps = 0.100000)

[05:13:46] [worker #0] ML tree search #17, logLikelihood: -99083.341038

[05:13:46 -566575.775051] Initial branch length optimization
[05:13:49 -420079.906929] Model parameter optimization (eps = 10.000000)
[05:14:18 -419364.954405] AUTODETECT spr round 1 (radius: 5)
[05:15:20 -230733.400776] AUTODETECT spr round 2 (radius: 10)
[05:16:28 -164637.541157] AUTODETECT spr round 3 (radius: 15)
[05:17:49 -127351.734505] AUTODETECT spr round 4 (radius: 20)
[05:19:19 -112727.118952] AUTODETECT spr round 5 (radius: 25)
[05:21:08 -110196.040613] SPR radius for FAST iterations: 25 (autodetect)
[05:21:08 -110196.040613] Model parameter optimization (eps = 3.000000)
[05:21:50 -109735.065044] FAST spr round 1 (radius: 25)
[05:23:13 -99771.339213] FAST spr round 2 (radius: 25)
[05:24:15 -99316.333272] FAST spr round 3 (radius: 25)
[05:25:11 -99303.165795] FAST spr round 4 (radius: 25)
[05:26:01 -99301.515518] FAST spr round 5 (radius: 25)
[05:26:50 -99301.514201] Model parameter optimization (eps = 1.000000)
[05:27:02 -99296.423431] SLOW spr round 1 (radius: 5)
[05:28:12 -99270.847428] SLOW spr round 2 (radius: 5)
[05:29:22 -99270.831974] SLOW spr round 3 (radius: 10)
[05:30:35 -99268.913863] SLOW spr round 4 (radius: 5)
[05:32:02 -99268.893336] SLOW spr round 5 (radius: 10)
[05:33:30 -99268.893269] SLOW spr round 6 (radius: 15)
[05:33:57] [worker #1] ML tree search #20, logLikelihood: -99083.650048
[05:35:16 -99268.765153] SLOW spr round 7 (radius: 5)
[05:36:45 -99268.765005] SLOW spr round 8 (radius: 10)
[05:38:14 -99268.764959] SLOW spr round 9 (radius: 15)
[05:39:58 -99268.764920] SLOW spr round 10 (radius: 20)
[05:42:30 -99268.764885] SLOW spr round 11 (radius: 25)
[05:45:29 -99268.764852] Model parameter optimization (eps = 0.100000)

[05:45:33] [worker #0] ML tree search #19, logLikelihood: -99268.748486


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.273220,0.600602) (0.129679,0.706185) (0.429611,0.846636) (0.167490,2.272391) 
   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: -99078.428843

AIC score: 200410.857686 / AICc score: 2742922.857686 / BIC score: 205677.664495
Free parameters (model + branch lengths): 1127

WARNING: Number of free parameters (K=1127) is larger than alignment size (n=791).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 136 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H7M6/3_mltree/Q9H7M6.raxml.log

Analysis started: 12-Jul-2021 08:19:08 / finished: 12-Jul-2021 14:04:42

Elapsed time: 20733.910 seconds