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 05-Jul-2021 16:05:12 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/2_msa/Q9UPV0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/3_mltree/Q9UPV0 --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/Q9UPV0/2_msa/Q9UPV0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 212 taxa and 78 sites

WARNING: Sequences tr_Q4QGP1_Q4QGP1_LEIMA_5664 and tr_A4H6W6_A4H6W6_LEIBR_5660 are exactly identical!
WARNING: Sequences sp_Q5DU05_CE164_MOUSE_10090 and tr_G3IAK5_G3IAK5_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q5DU05_CE164_MOUSE_10090 and tr_M0R9A9_M0R9A9_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q5DU05_CE164_MOUSE_10090 and tr_A0A3Q0CP20_A0A3Q0CP20_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3XZ27_M3XZ27_MUSPF_9669 and tr_A0A2Y9KH76_A0A2Y9KH76_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_H2NFF0_H2NFF0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_K7D7G7_K7D7G7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_F7CQ41_F7CQ41_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_G7PP21_G7PP21_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_A0A096MNP8_A0A096MNP8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_A0A2K5MIV4_A0A2K5MIV4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_A0A2K6BN83_A0A2K6BN83_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_A0A2K5YNH3_A0A2K5YNH3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QUA8_G3QUA8_GORGO_9595 and tr_A0A2R9AMB4_A0A2R9AMB4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F1PB71_F1PB71_CANLF_9615 and tr_G3UFI2_G3UFI2_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_F1PB71_F1PB71_CANLF_9615 and tr_A0A2Y9RMN1_A0A2Y9RMN1_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_Q4CW09_Q4CW09_TRYCC_353153 and tr_Q4DF76_Q4DF76_TRYCC_353153 are exactly identical!
WARNING: Sequences tr_Q4E2M4_Q4E2M4_TRYCC_353153 and tr_Q4E5M3_Q4E5M3_TRYCC_353153 are exactly identical!
WARNING: Sequences tr_A0A158NIY8_A0A158NIY8_ATTCE_12957 and tr_F4WUD2_F4WUD2_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NIY8_A0A158NIY8_ATTCE_12957 and tr_A0A195BXE6_A0A195BXE6_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NIY8_A0A158NIY8_ATTCE_12957 and tr_A0A195FBU2_A0A195FBU2_9HYME_34720 are exactly identical!
WARNING: Sequences tr_I3MH88_I3MH88_ICTTR_43179 and tr_L5KK07_L5KK07_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_I3MH88_I3MH88_ICTTR_43179 and tr_A0A384C1D6_A0A384C1D6_URSMA_29073 are exactly identical!
WARNING: Sequences tr_H0YPJ2_H0YPJ2_TAEGU_59729 and tr_A0A218UPM4_A0A218UPM4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_R1BJN7_R1BJN7_EMIHU_2903 and tr_R1E2D4_R1E2D4_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_W2PDH2_W2PDH2_PHYPN_761204 and tr_W2LW18_W2LW18_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PDH2_W2PDH2_PHYPN_761204 and tr_A0A329RM85_A0A329RM85_9STRA_29920 are exactly identical!
WARNING: Sequences tr_W2RDV8_W2RDV8_PHYPN_761204 and tr_A0A0W8CN73_A0A0W8CN73_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RDV8_W2RDV8_PHYPN_761204 and tr_W2M400_W2M400_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067CJS1_A0A067CJS1_SAPPC_695850 and tr_T0RG99_T0RG99_9STRA_1156394 are exactly identical!
WARNING: Sequences tr_A0A1S3SYP5_A0A1S3SYP5_SALSA_8030 and tr_A0A060VVM5_A0A060VVM5_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1D1VRZ2_A0A1D1VRZ2_RAMVA_947166 and tr_A0A1D1VS15_A0A1D1VS15_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VRZ2_A0A1D1VRZ2_RAMVA_947166 and tr_A0A1D1VS39_A0A1D1VS39_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VRZ2_A0A1D1VRZ2_RAMVA_947166 and tr_A0A1D1VTM8_A0A1D1VTM8_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VRZ2_A0A1D1VRZ2_RAMVA_947166 and tr_A0A1D1VVR9_A0A1D1VVR9_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VRZ2_A0A1D1VRZ2_RAMVA_947166 and tr_A0A1D1VZ95_A0A1D1VZ95_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A226N4Y8_A0A226N4Y8_CALSU_9009 and tr_A0A226PPB8_A0A226PPB8_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 37

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/Q9UPV0/3_mltree/Q9UPV0.raxml.reduced.phy

Alignment comprises 1 partitions and 78 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 78 / 78
Gaps: 3.05 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/3_mltree/Q9UPV0.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 212 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -22608.385012] Initial branch length optimization
[00:00:00 -17826.848956] Model parameter optimization (eps = 10.000000)
[00:00:04 -17775.818705] AUTODETECT spr round 1 (radius: 5)
[00:00:10 -14175.777483] AUTODETECT spr round 2 (radius: 10)
[00:00:16 -12633.933921] AUTODETECT spr round 3 (radius: 15)
[00:00:24 -10881.936793] AUTODETECT spr round 4 (radius: 20)
[00:00:32 -10375.343418] AUTODETECT spr round 5 (radius: 25)
[00:00:40 -10201.244443] SPR radius for FAST iterations: 25 (autodetect)
[00:00:40 -10201.244443] Model parameter optimization (eps = 3.000000)
[00:00:45 -10150.974511] FAST spr round 1 (radius: 25)
[00:00:53 -8902.721639] FAST spr round 2 (radius: 25)
[00:00:59 -8836.696741] FAST spr round 3 (radius: 25)
[00:01:05 -8832.284948] FAST spr round 4 (radius: 25)
[00:01:10 -8832.283893] Model parameter optimization (eps = 1.000000)
[00:01:12 -8830.746208] SLOW spr round 1 (radius: 5)
[00:01:21 -8827.984440] SLOW spr round 2 (radius: 5)
[00:01:30 -8827.772841] SLOW spr round 3 (radius: 5)
[00:01:39 -8827.771926] SLOW spr round 4 (radius: 10)
[00:01:47 -8825.974232] SLOW spr round 5 (radius: 5)
[00:01:58 -8822.819767] SLOW spr round 6 (radius: 5)
[00:02:08 -8822.819534] SLOW spr round 7 (radius: 10)
[00:02:16 -8822.819398] SLOW spr round 8 (radius: 15)
[00:02:28 -8822.522635] SLOW spr round 9 (radius: 5)
[00:02:40 -8822.328810] SLOW spr round 10 (radius: 5)
[00:02:49 -8822.328333] SLOW spr round 11 (radius: 10)
[00:02:56 -8822.328088] SLOW spr round 12 (radius: 15)
[00:03:08 -8822.327913] SLOW spr round 13 (radius: 20)
[00:03:21 -8822.327760] SLOW spr round 14 (radius: 25)
[00:03:33 -8822.327611] Model parameter optimization (eps = 0.100000)

[00:03:33] [worker #0] ML tree search #1, logLikelihood: -8822.284151

[00:03:33 -22262.387352] Initial branch length optimization
[00:03:34 -17844.131385] Model parameter optimization (eps = 10.000000)
[00:03:39 -17800.781937] AUTODETECT spr round 1 (radius: 5)
[00:03:43 -14520.303791] AUTODETECT spr round 2 (radius: 10)
[00:03:48 -12062.908572] AUTODETECT spr round 3 (radius: 15)
[00:03:57 -10842.536771] AUTODETECT spr round 4 (radius: 20)
[00:04:07 -10042.955779] AUTODETECT spr round 5 (radius: 25)
[00:04:11] [worker #1] ML tree search #2, logLikelihood: -8818.282753
[00:04:17 -9985.979131] SPR radius for FAST iterations: 25 (autodetect)
[00:04:17 -9985.979131] Model parameter optimization (eps = 3.000000)
[00:04:22 -9957.177894] FAST spr round 1 (radius: 25)
[00:04:29 -8984.721079] FAST spr round 2 (radius: 25)
[00:04:37 -8850.163956] FAST spr round 3 (radius: 25)
[00:04:43 -8841.069068] FAST spr round 4 (radius: 25)
[00:04:48 -8840.619737] FAST spr round 5 (radius: 25)
[00:04:53 -8840.619737] Model parameter optimization (eps = 1.000000)
[00:04:57 -8836.447271] SLOW spr round 1 (radius: 5)
[00:05:07 -8830.438602] SLOW spr round 2 (radius: 5)
[00:05:16 -8830.021631] SLOW spr round 3 (radius: 5)
[00:05:24 -8830.021004] SLOW spr round 4 (radius: 10)
[00:05:32 -8829.587384] SLOW spr round 5 (radius: 5)
[00:05:42 -8828.217485] SLOW spr round 6 (radius: 5)
[00:05:50 -8827.941507] SLOW spr round 7 (radius: 5)
[00:05:59 -8827.941479] SLOW spr round 8 (radius: 10)
[00:06:08 -8827.941478] SLOW spr round 9 (radius: 15)
[00:06:22 -8827.385241] SLOW spr round 10 (radius: 5)
[00:06:34 -8827.114289] SLOW spr round 11 (radius: 5)
[00:06:43 -8827.114233] SLOW spr round 12 (radius: 10)
[00:06:51 -8827.114233] SLOW spr round 13 (radius: 15)
[00:07:04 -8827.114233] SLOW spr round 14 (radius: 20)
[00:07:16 -8827.114233] SLOW spr round 15 (radius: 25)
[00:07:27 -8826.802002] SLOW spr round 16 (radius: 5)
[00:07:37 -8826.799528] SLOW spr round 17 (radius: 10)
[00:07:47 -8826.798633] SLOW spr round 18 (radius: 15)
[00:07:59 -8826.798306] SLOW spr round 19 (radius: 20)
[00:08:11 -8826.798186] SLOW spr round 20 (radius: 25)
[00:08:21 -8826.798141] Model parameter optimization (eps = 0.100000)

[00:08:23] [worker #0] ML tree search #3, logLikelihood: -8826.542344

[00:08:23 -22714.654163] Initial branch length optimization
[00:08:23 -17864.184297] Model parameter optimization (eps = 10.000000)
[00:08:27 -17804.375460] AUTODETECT spr round 1 (radius: 5)
[00:08:32 -14518.095557] AUTODETECT spr round 2 (radius: 10)
[00:08:38 -12384.283668] AUTODETECT spr round 3 (radius: 15)
[00:08:46 -11079.287356] AUTODETECT spr round 4 (radius: 20)
[00:08:46] [worker #1] ML tree search #4, logLikelihood: -8817.566141
[00:08:55 -10501.587705] AUTODETECT spr round 5 (radius: 25)
[00:09:03 -10084.459252] SPR radius for FAST iterations: 25 (autodetect)
[00:09:03 -10084.459252] Model parameter optimization (eps = 3.000000)
[00:09:08 -10032.798054] FAST spr round 1 (radius: 25)
[00:09:16 -8919.499703] FAST spr round 2 (radius: 25)
[00:09:23 -8841.331621] FAST spr round 3 (radius: 25)
[00:09:28 -8830.468167] FAST spr round 4 (radius: 25)
[00:09:34 -8826.593433] FAST spr round 5 (radius: 25)
[00:09:38 -8826.457846] FAST spr round 6 (radius: 25)
[00:09:43 -8826.457809] Model parameter optimization (eps = 1.000000)
[00:09:45 -8825.660996] SLOW spr round 1 (radius: 5)
[00:09:54 -8819.787849] SLOW spr round 2 (radius: 5)
[00:10:03 -8819.009782] SLOW spr round 3 (radius: 5)
[00:10:11 -8819.009671] SLOW spr round 4 (radius: 10)
[00:10:19 -8818.769675] SLOW spr round 5 (radius: 5)
[00:10:30 -8818.767675] SLOW spr round 6 (radius: 10)
[00:10:40 -8818.767448] SLOW spr round 7 (radius: 15)
[00:10:51 -8818.767414] SLOW spr round 8 (radius: 20)
[00:11:03 -8818.767409] SLOW spr round 9 (radius: 25)
[00:11:15 -8818.767408] Model parameter optimization (eps = 0.100000)

[00:11:17] [worker #0] ML tree search #5, logLikelihood: -8818.675403

[00:11:17 -22551.900726] Initial branch length optimization
[00:11:17 -17836.613482] Model parameter optimization (eps = 10.000000)
[00:11:21 -17793.485729] AUTODETECT spr round 1 (radius: 5)
[00:11:26 -14247.965493] AUTODETECT spr round 2 (radius: 10)
[00:11:34 -11540.837140] AUTODETECT spr round 3 (radius: 15)
[00:11:42 -10395.930800] AUTODETECT spr round 4 (radius: 20)
[00:11:50 -10094.285938] AUTODETECT spr round 5 (radius: 25)
[00:11:59 -10089.434995] SPR radius for FAST iterations: 25 (autodetect)
[00:11:59 -10089.434995] Model parameter optimization (eps = 3.000000)
[00:12:03 -10051.037899] FAST spr round 1 (radius: 25)
[00:12:10 -8875.297935] FAST spr round 2 (radius: 25)
[00:12:17 -8829.037117] FAST spr round 3 (radius: 25)
[00:12:21 -8828.055508] FAST spr round 4 (radius: 25)
[00:12:26 -8828.055017] Model parameter optimization (eps = 1.000000)
[00:12:28] [worker #1] ML tree search #6, logLikelihood: -8822.420906
[00:12:29 -8826.294535] SLOW spr round 1 (radius: 5)
[00:12:36 -8824.952149] SLOW spr round 2 (radius: 5)
[00:12:45 -8824.951943] SLOW spr round 3 (radius: 10)
[00:12:53 -8824.951905] SLOW spr round 4 (radius: 15)
[00:13:06 -8820.956458] SLOW spr round 5 (radius: 5)
[00:13:18 -8819.966398] SLOW spr round 6 (radius: 5)
[00:13:28 -8819.966305] SLOW spr round 7 (radius: 10)
[00:13:36 -8819.966304] SLOW spr round 8 (radius: 15)
[00:13:48 -8819.966303] SLOW spr round 9 (radius: 20)
[00:14:02 -8819.966303] SLOW spr round 10 (radius: 25)
[00:14:14 -8819.966303] Model parameter optimization (eps = 0.100000)

[00:14:15] [worker #0] ML tree search #7, logLikelihood: -8819.889892

[00:14:15 -22242.946135] Initial branch length optimization
[00:14:15 -17645.841023] Model parameter optimization (eps = 10.000000)
[00:14:19 -17605.185856] AUTODETECT spr round 1 (radius: 5)
[00:14:24 -14745.388643] AUTODETECT spr round 2 (radius: 10)
[00:14:32 -12203.965336] AUTODETECT spr round 3 (radius: 15)
[00:14:41 -10846.895684] AUTODETECT spr round 4 (radius: 20)
[00:14:49 -10229.658158] AUTODETECT spr round 5 (radius: 25)
[00:14:58 -10033.349496] SPR radius for FAST iterations: 25 (autodetect)
[00:14:58 -10033.349496] Model parameter optimization (eps = 3.000000)
[00:15:02 -9993.935755] FAST spr round 1 (radius: 25)
[00:15:09 -8897.548459] FAST spr round 2 (radius: 25)
[00:15:15 -8860.975777] FAST spr round 3 (radius: 25)
[00:15:21 -8855.932127] FAST spr round 4 (radius: 25)
[00:15:26 -8851.546877] FAST spr round 5 (radius: 25)
[00:15:31 -8851.546745] Model parameter optimization (eps = 1.000000)
[00:15:33 -8850.279753] SLOW spr round 1 (radius: 5)
[00:15:42 -8850.003034] SLOW spr round 2 (radius: 5)
[00:15:50 -8850.002658] SLOW spr round 3 (radius: 10)
[00:15:59 -8848.447606] SLOW spr round 4 (radius: 5)
[00:16:10 -8848.355739] SLOW spr round 5 (radius: 10)
[00:16:20 -8848.355500] SLOW spr round 6 (radius: 15)
[00:16:33 -8848.355466] SLOW spr round 7 (radius: 20)
[00:16:46 -8840.224682] SLOW spr round 8 (radius: 5)
[00:16:59 -8832.527863] SLOW spr round 9 (radius: 5)
[00:17:09 -8827.332263] SLOW spr round 10 (radius: 5)
[00:17:18 -8822.373599] SLOW spr round 11 (radius: 5)
[00:17:25 -8822.373476] SLOW spr round 12 (radius: 10)
[00:17:32 -8822.373467] SLOW spr round 13 (radius: 15)
[00:17:45 -8822.373466] SLOW spr round 14 (radius: 20)
[00:17:56 -8822.373466] SLOW spr round 15 (radius: 25)
[00:18:06 -8822.373466] Model parameter optimization (eps = 0.100000)

[00:18:08] [worker #0] ML tree search #9, logLikelihood: -8822.046155

[00:18:08 -22707.967582] Initial branch length optimization
[00:18:08 -17938.789346] Model parameter optimization (eps = 10.000000)
[00:18:12 -17886.682141] AUTODETECT spr round 1 (radius: 5)
[00:18:17 -14401.952546] AUTODETECT spr round 2 (radius: 10)
[00:18:24 -12267.951318] AUTODETECT spr round 3 (radius: 15)
[00:18:33 -10399.534452] AUTODETECT spr round 4 (radius: 20)
[00:18:43 -9745.850824] AUTODETECT spr round 5 (radius: 25)
[00:18:52 -9732.028375] SPR radius for FAST iterations: 25 (autodetect)
[00:18:52 -9732.028375] Model parameter optimization (eps = 3.000000)
[00:18:56 -9675.478649] FAST spr round 1 (radius: 25)
[00:19:03 -8895.195063] FAST spr round 2 (radius: 25)
[00:19:10 -8841.762247] FAST spr round 3 (radius: 25)
[00:19:15 -8838.598138] FAST spr round 4 (radius: 25)
[00:19:20 -8838.586384] Model parameter optimization (eps = 1.000000)
[00:19:23 -8837.087990] SLOW spr round 1 (radius: 5)
[00:19:33 -8833.889726] SLOW spr round 2 (radius: 5)
[00:19:42 -8833.490219] SLOW spr round 3 (radius: 5)
[00:19:50 -8831.881392] SLOW spr round 4 (radius: 5)
[00:19:59 -8828.665801] SLOW spr round 5 (radius: 5)
[00:20:06 -8828.655581] SLOW spr round 6 (radius: 10)
[00:20:13 -8827.807889] SLOW spr round 7 (radius: 5)
[00:20:24 -8827.807845] SLOW spr round 8 (radius: 10)
[00:20:34 -8826.792556] SLOW spr round 9 (radius: 5)
[00:20:45 -8826.792029] SLOW spr round 10 (radius: 10)
[00:20:54 -8826.792001] SLOW spr round 11 (radius: 15)
[00:21:04] [worker #1] ML tree search #8, logLikelihood: -8831.347305
[00:21:06 -8826.791997] SLOW spr round 12 (radius: 20)
[00:21:17 -8826.791996] SLOW spr round 13 (radius: 25)
[00:21:29 -8825.839424] SLOW spr round 14 (radius: 5)
[00:21:41 -8825.833967] SLOW spr round 15 (radius: 10)
[00:21:52 -8825.833872] SLOW spr round 16 (radius: 15)
[00:22:02 -8825.833850] SLOW spr round 17 (radius: 20)
[00:22:13 -8825.833845] SLOW spr round 18 (radius: 25)
[00:22:26 -8825.833844] Model parameter optimization (eps = 0.100000)

[00:22:27] [worker #0] ML tree search #11, logLikelihood: -8825.621719

[00:22:27 -22614.912140] Initial branch length optimization
[00:22:28 -17931.032834] Model parameter optimization (eps = 10.000000)
[00:22:33 -17875.582908] AUTODETECT spr round 1 (radius: 5)
[00:22:38 -13990.529813] AUTODETECT spr round 2 (radius: 10)
[00:22:45 -11620.547585] AUTODETECT spr round 3 (radius: 15)
[00:22:53 -11091.819583] AUTODETECT spr round 4 (radius: 20)
[00:23:03 -10149.677870] AUTODETECT spr round 5 (radius: 25)
[00:23:11 -10144.933198] SPR radius for FAST iterations: 25 (autodetect)
[00:23:11 -10144.933198] Model parameter optimization (eps = 3.000000)
[00:23:14 -10104.101810] FAST spr round 1 (radius: 25)
[00:23:21 -8927.198150] FAST spr round 2 (radius: 25)
[00:23:27 -8837.524865] FAST spr round 3 (radius: 25)
[00:23:32 -8836.197248] FAST spr round 4 (radius: 25)
[00:23:38 -8836.196217] Model parameter optimization (eps = 1.000000)
[00:23:40 -8833.074747] SLOW spr round 1 (radius: 5)
[00:23:49 -8830.624858] SLOW spr round 2 (radius: 5)
[00:23:58 -8830.624201] SLOW spr round 3 (radius: 10)
[00:24:06 -8829.038399] SLOW spr round 4 (radius: 5)
[00:24:14] [worker #1] ML tree search #10, logLikelihood: -8819.230457
[00:24:17 -8829.038294] SLOW spr round 5 (radius: 10)
[00:24:27 -8829.038283] SLOW spr round 6 (radius: 15)
[00:24:38 -8829.038281] SLOW spr round 7 (radius: 20)
[00:24:50 -8829.038281] SLOW spr round 8 (radius: 25)
[00:25:01 -8829.009180] Model parameter optimization (eps = 0.100000)

[00:25:02] [worker #0] ML tree search #13, logLikelihood: -8828.904292

[00:25:02 -22293.456853] Initial branch length optimization
[00:25:03 -17741.393084] Model parameter optimization (eps = 10.000000)
[00:25:07 -17685.048046] AUTODETECT spr round 1 (radius: 5)
[00:25:12 -14339.650571] AUTODETECT spr round 2 (radius: 10)
[00:25:19 -12525.527026] AUTODETECT spr round 3 (radius: 15)
[00:25:27 -11222.446665] AUTODETECT spr round 4 (radius: 20)
[00:25:34 -10628.661583] AUTODETECT spr round 5 (radius: 25)
[00:25:41 -10412.297555] SPR radius for FAST iterations: 25 (autodetect)
[00:25:41 -10412.297555] Model parameter optimization (eps = 3.000000)
[00:25:45 -10365.115600] FAST spr round 1 (radius: 25)
[00:25:52 -9011.066053] FAST spr round 2 (radius: 25)
[00:26:00 -8852.649230] FAST spr round 3 (radius: 25)
[00:26:06 -8834.956771] FAST spr round 4 (radius: 25)
[00:26:11 -8834.956692] Model parameter optimization (eps = 1.000000)
[00:26:14 -8830.267075] SLOW spr round 1 (radius: 5)
[00:26:22 -8824.401720] SLOW spr round 2 (radius: 5)
[00:26:30 -8820.773252] SLOW spr round 3 (radius: 5)
[00:26:39 -8820.771384] SLOW spr round 4 (radius: 10)
[00:26:47 -8820.770727] SLOW spr round 5 (radius: 15)
[00:27:02 -8820.770434] SLOW spr round 6 (radius: 20)
[00:27:15 -8820.770307] SLOW spr round 7 (radius: 25)
[00:27:28 -8820.770254] Model parameter optimization (eps = 0.100000)

[00:27:29] [worker #0] ML tree search #15, logLikelihood: -8820.694588

[00:27:29 -22280.475460] Initial branch length optimization
[00:27:29 -17819.905289] Model parameter optimization (eps = 10.000000)
[00:27:34 -17772.996752] AUTODETECT spr round 1 (radius: 5)
[00:27:39 -14410.408997] AUTODETECT spr round 2 (radius: 10)
[00:27:40] [worker #1] ML tree search #12, logLikelihood: -8815.156915
[00:27:46 -11777.439050] AUTODETECT spr round 3 (radius: 15)
[00:27:54 -10442.169731] AUTODETECT spr round 4 (radius: 20)
[00:28:03 -10087.892348] AUTODETECT spr round 5 (radius: 25)
[00:28:11 -10086.100240] SPR radius for FAST iterations: 25 (autodetect)
[00:28:11 -10086.100240] Model parameter optimization (eps = 3.000000)
[00:28:15 -10065.348657] FAST spr round 1 (radius: 25)
[00:28:22 -8895.447088] FAST spr round 2 (radius: 25)
[00:28:28 -8846.878819] FAST spr round 3 (radius: 25)
[00:28:34 -8838.405114] FAST spr round 4 (radius: 25)
[00:28:39 -8838.311159] Model parameter optimization (eps = 1.000000)
[00:28:42 -8824.894154] SLOW spr round 1 (radius: 5)
[00:28:51 -8822.554499] SLOW spr round 2 (radius: 5)
[00:28:59 -8822.029069] SLOW spr round 3 (radius: 5)
[00:29:09 -8821.636928] SLOW spr round 4 (radius: 5)
[00:29:18 -8821.636756] SLOW spr round 5 (radius: 10)
[00:29:26 -8821.256572] SLOW spr round 6 (radius: 5)
[00:29:37 -8821.256460] SLOW spr round 7 (radius: 10)
[00:29:46 -8819.571371] SLOW spr round 8 (radius: 5)
[00:29:57 -8817.765849] SLOW spr round 9 (radius: 5)
[00:30:06 -8817.765687] SLOW spr round 10 (radius: 10)
[00:30:15 -8817.765685] SLOW spr round 11 (radius: 15)
[00:30:27 -8817.765684] SLOW spr round 12 (radius: 20)
[00:30:41 -8817.765684] SLOW spr round 13 (radius: 25)
[00:30:55 -8817.765684] Model parameter optimization (eps = 0.100000)

[00:30:57] [worker #0] ML tree search #17, logLikelihood: -8817.363109

[00:30:57 -22663.074709] Initial branch length optimization
[00:30:58 -17866.630536] Model parameter optimization (eps = 10.000000)
[00:31:01 -17802.221701] AUTODETECT spr round 1 (radius: 5)
[00:31:06 -14011.608630] AUTODETECT spr round 2 (radius: 10)
[00:31:14 -11891.686008] AUTODETECT spr round 3 (radius: 15)
[00:31:22 -10317.117984] AUTODETECT spr round 4 (radius: 20)
[00:31:31 -10062.054748] AUTODETECT spr round 5 (radius: 25)
[00:31:40 -9692.032170] SPR radius for FAST iterations: 25 (autodetect)
[00:31:40 -9692.032170] Model parameter optimization (eps = 3.000000)
[00:31:44 -9630.656002] FAST spr round 1 (radius: 25)
[00:31:50 -8923.071953] FAST spr round 2 (radius: 25)
[00:31:55 -8841.118191] FAST spr round 3 (radius: 25)
[00:31:59 -8831.878998] FAST spr round 4 (radius: 25)
[00:32:03 -8831.878585] Model parameter optimization (eps = 1.000000)
[00:32:06 -8830.350270] SLOW spr round 1 (radius: 5)
[00:32:15 -8829.765335] SLOW spr round 2 (radius: 5)
[00:32:24 -8829.096490] SLOW spr round 3 (radius: 5)
[00:32:32 -8829.096168] SLOW spr round 4 (radius: 10)
[00:32:38 -8829.076241] SLOW spr round 5 (radius: 15)
[00:32:48 -8829.062531] SLOW spr round 6 (radius: 20)
[00:32:59 -8828.820861] SLOW spr round 7 (radius: 5)
[00:33:12 -8826.402326] SLOW spr round 8 (radius: 5)
[00:33:23 -8825.454805] SLOW spr round 9 (radius: 5)
[00:33:32 -8825.454648] SLOW spr round 10 (radius: 10)
[00:33:41 -8825.454639] SLOW spr round 11 (radius: 15)
[00:33:46] [worker #1] ML tree search #14, logLikelihood: -8819.071748
[00:33:53 -8825.454637] SLOW spr round 12 (radius: 20)
[00:34:06 -8825.454637] SLOW spr round 13 (radius: 25)
[00:34:19 -8825.454637] Model parameter optimization (eps = 0.100000)

[00:34:20] [worker #0] ML tree search #19, logLikelihood: -8825.437845

[00:37:02] [worker #1] ML tree search #16, logLikelihood: -8818.715956
[00:39:36] [worker #1] ML tree search #18, logLikelihood: -8827.794926
[00:43:18] [worker #1] ML tree search #20, logLikelihood: -8824.682460

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.283824,0.300755) (0.191903,0.732890) (0.273595,0.841432) (0.250678,2.169248) 
   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: -8815.156915

AIC score: 18484.313831 / AICc score: 383996.313831 / BIC score: 19490.628500
Free parameters (model + branch lengths): 427

WARNING: Number of free parameters (K=427) is larger than alignment size (n=78).
         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/Q9UPV0/3_mltree/Q9UPV0.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/3_mltree/Q9UPV0.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/3_mltree/Q9UPV0.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPV0/3_mltree/Q9UPV0.raxml.log

Analysis started: 05-Jul-2021 16:05:12 / finished: 05-Jul-2021 16:48:30

Elapsed time: 2598.587 seconds

Consumed energy: 195.533 Wh