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 04-Jul-2021 09:26:11 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/2_msa/P20023_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/3_mltree/P20023 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/2_msa/P20023_trimmed_msa.fasta [00:00:00] Loaded alignment with 855 taxa and 196 sites WARNING: Sequences tr_B4QH67_B4QH67_DROSI_7240 and sp_Q09101_HIG_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QH67_B4QH67_DROSI_7240 and tr_B4HSP9_B4HSP9_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QH67_B4QH67_DROSI_7240 and tr_A0A1W4UK55_A0A1W4UK55_DROFC_30025 are exactly identical! WARNING: Sequences tr_B4K316_B4K316_DROGR_7222 and tr_B4KI98_B4KI98_DROMO_7230 are exactly identical! WARNING: Sequences tr_G3HTB4_G3HTB4_CRIGR_10029 and tr_A0A1U8C706_A0A1U8C706_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and sp_Q9BYH1_SE6L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and tr_G7PHF4_G7PHF4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and tr_A0A096N6T9_A0A096N6T9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and tr_A0A0D9RCL1_A0A0D9RCL1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and tr_A0A2K6BB48_A0A2K6BB48_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2ZIJ9_A0A2I2ZIJ9_GORGO_9595 and tr_A0A2K6A445_A0A2K6A445_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QD59_G3QD59_GORGO_9595 and sp_P15529_MCP_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PFF4_H2PFF4_PONAB_9601 and sp_Q5RAD0_CO7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1N4Q5_G1N4Q5_MELGA_9103 and tr_A0A091WGI3_A0A091WGI3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H2Q115_H2Q115_PANTR_9598 and sp_P20023_CR2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q115_H2Q115_PANTR_9598 and tr_A0A2R8ZSE1_A0A2R8ZSE1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QZS3_H2QZS3_PANTR_9598 and sp_P10643_CO7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QZS3_H2QZS3_PANTR_9598 and tr_A0A2R9AYC3_A0A2R9AYC3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RBN8_H2RBN8_PANTR_9598 and tr_A0A2R9BSA1_A0A2R9BSA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5NY78_W5NY78_SHEEP_9940 and tr_G3N0S9_G3N0S9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4AW05_M4AW05_XIPMA_8083 and tr_A0A087YKK6_A0A087YKK6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2C9F1E0_A0A2C9F1E0_CAVPO_10141 and sp_P70105_MCP_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A1D5QPW5_A0A1D5QPW5_MACMU_9544 and tr_A0A2K5LFN3_A0A2K5LFN3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QPW5_A0A1D5QPW5_MACMU_9544 and tr_A0A2K5XLU6_A0A2K5XLU6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DTG7_F7DTG7_MACMU_9544 and tr_G7NUP4_G7NUP4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GSR2_F7GSR2_MACMU_9544 and tr_G8F4J7_G8F4J7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GSR2_F7GSR2_MACMU_9544 and tr_A0A2K6DKP6_A0A2K6DKP6_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZBE0_H0ZBE0_TAEGU_59729 and tr_A0A218V5G6_A0A218V5G6_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A287AH22_A0A287AH22_PIG_9823 and sp_O02839_MCP_PIG_9823 are exactly identical! WARNING: Sequences tr_F1SMJ1_F1SMJ1_PIG_9823 and sp_Q9TUQ3_CO7_PIG_9823 are exactly identical! WARNING: Sequences tr_G1MI83_G1MI83_AILME_9646 and tr_A0A384BS25_A0A384BS25_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P7E9_G7P7E9_MACFA_9541 and tr_A0A096NBN3_A0A096NBN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7P7E9_G7P7E9_MACFA_9541 and tr_A0A2K5L1N9_A0A2K5L1N9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F1N045_F1N045_BOVIN_9913 and sp_Q29RQ1_CO7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3M5A8_A0A2I3M5A8_PAPAN_9555 and tr_A0A2K5KVB6_A0A2K5KVB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3M5A8_A0A2I3M5A8_PAPAN_9555 and tr_A0A2K6E0I3_A0A2K6E0I3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N448_A0A2I3N448_PAPAN_9555 and tr_A0A2K5ZWK4_A0A2K5ZWK4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1S3QHG9_A0A1S3QHG9_SALSA_8030 and tr_A0A1S3QU73_A0A1S3QU73_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2K5LCB9_A0A2K5LCB9_CERAT_9531 and tr_A0A2K6A0I5_A0A2K6A0I5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4CQH8_A0A2U4CQH8_TURTR_9739 and tr_A0A2Y9PVM3_A0A2Y9PVM3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CQH8_A0A2U4CQH8_TURTR_9739 and tr_A0A383Z8S9_A0A383Z8S9_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 41 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/P20023/3_mltree/P20023.raxml.reduced.phy Alignment comprises 1 partitions and 196 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 196 / 196 Gaps: 20.03 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/3_mltree/P20023.raxml.rba Parallelization scheme autoconfig: 4 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 855 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -302276.948772] Initial branch length optimization [00:00:05 -259757.370668] Model parameter optimization (eps = 10.000000) [00:00:44 -258688.552823] AUTODETECT spr round 1 (radius: 5) [00:02:46 -205529.823572] AUTODETECT spr round 2 (radius: 10) [00:05:10 -165845.422476] AUTODETECT spr round 3 (radius: 15) [00:07:51 -144555.813231] AUTODETECT spr round 4 (radius: 20) [00:11:17 -132989.432411] AUTODETECT spr round 5 (radius: 25) [00:15:39 -130194.507237] SPR radius for FAST iterations: 25 (autodetect) [00:15:39 -130194.507237] Model parameter optimization (eps = 3.000000) [00:16:00 -130140.576219] FAST spr round 1 (radius: 25) [00:20:03 -118404.668293] FAST spr round 2 (radius: 25) [00:22:54 -117496.034746] FAST spr round 3 (radius: 25) [00:25:19 -117301.941547] FAST spr round 4 (radius: 25) [00:27:21 -117271.310797] FAST spr round 5 (radius: 25) [00:29:08 -117264.631206] FAST spr round 6 (radius: 25) [00:30:52 -117206.082595] FAST spr round 7 (radius: 25) [00:32:33 -117196.916951] FAST spr round 8 (radius: 25) [00:34:08 -117196.915838] Model parameter optimization (eps = 1.000000) [00:34:15 -117196.634243] SLOW spr round 1 (radius: 5) [00:36:22 -117174.752315] SLOW spr round 2 (radius: 5) [00:38:31 -117172.903657] SLOW spr round 3 (radius: 5) [00:40:36 -117172.352959] SLOW spr round 4 (radius: 5) [00:42:38 -117172.352762] SLOW spr round 5 (radius: 10) [00:44:54 -117167.338734] SLOW spr round 6 (radius: 5) [00:47:24 -117162.068055] SLOW spr round 7 (radius: 5) [00:49:36 -117159.252079] SLOW spr round 8 (radius: 5) [00:51:42 -117158.407531] SLOW spr round 9 (radius: 5) [00:53:43 -117158.407472] SLOW spr round 10 (radius: 10) [00:56:02 -117149.598538] SLOW spr round 11 (radius: 5) [00:58:31 -117141.644004] SLOW spr round 12 (radius: 5) [01:00:42 -117141.167114] SLOW spr round 13 (radius: 5) [01:02:45 -117141.166625] SLOW spr round 14 (radius: 10) [01:05:01 -117141.096956] SLOW spr round 15 (radius: 15) [01:09:01] [worker #1] ML tree search #2, logLikelihood: -117103.160255 [01:09:19 -117139.722413] SLOW spr round 16 (radius: 5) [01:11:56 -117135.861298] SLOW spr round 17 (radius: 5) [01:14:12 -117133.698142] SLOW spr round 18 (radius: 5) [01:16:19 -117133.662220] SLOW spr round 19 (radius: 10) [01:18:37 -117133.217201] SLOW spr round 20 (radius: 5) [01:21:00 -117133.107626] SLOW spr round 21 (radius: 5) [01:23:06 -117133.106407] SLOW spr round 22 (radius: 10) [01:25:19 -117133.106355] SLOW spr round 23 (radius: 15) [01:29:15 -117133.106351] SLOW spr round 24 (radius: 20) [01:32:56] [worker #2] ML tree search #3, logLikelihood: -117126.442954 [01:35:34 -117133.106350] SLOW spr round 25 (radius: 25) [01:43:31 -117133.106350] Model parameter optimization (eps = 0.100000) [01:43:35] [worker #0] ML tree search #1, logLikelihood: -117133.103781 [01:43:35 -303321.736311] Initial branch length optimization [01:43:40 -259681.500342] Model parameter optimization (eps = 10.000000) [01:44:12 -259095.110596] AUTODETECT spr round 1 (radius: 5) [01:46:07 -202019.132572] AUTODETECT spr round 2 (radius: 10) [01:48:21 -159996.759614] AUTODETECT spr round 3 (radius: 15) [01:50:52 -139495.094146] AUTODETECT spr round 4 (radius: 20) [01:54:23 -131629.498740] AUTODETECT spr round 5 (radius: 25) [01:59:04 -129716.040188] SPR radius for FAST iterations: 25 (autodetect) [01:59:04 -129716.040188] Model parameter optimization (eps = 3.000000) [01:59:29 -129675.527919] FAST spr round 1 (radius: 25) [02:03:28 -117830.398968] FAST spr round 2 (radius: 25) [02:06:09 -117242.613318] FAST spr round 3 (radius: 25) [02:08:18 -117200.534954] FAST spr round 4 (radius: 25) [02:10:12 -117182.304888] FAST spr round 5 (radius: 25) [02:12:08 -117178.515997] FAST spr round 6 (radius: 25) [02:13:58 -117178.515394] Model parameter optimization (eps = 1.000000) [02:14:10 -117177.268717] SLOW spr round 1 (radius: 5) [02:16:37 -117141.259528] SLOW spr round 2 (radius: 5) [02:18:55 -117139.617562] SLOW spr round 3 (radius: 5) [02:21:10 -117139.614705] SLOW spr round 4 (radius: 10) [02:23:42 -117136.754919] SLOW spr round 5 (radius: 5) [02:26:25 -117136.608669] SLOW spr round 6 (radius: 5) [02:28:51 -117136.607389] SLOW spr round 7 (radius: 10) [02:31:30 -117136.558253] SLOW spr round 8 (radius: 15) [02:36:08 -117135.417244] SLOW spr round 9 (radius: 5) [02:39:00 -117133.947902] SLOW spr round 10 (radius: 5) [02:41:30 -117133.946167] SLOW spr round 11 (radius: 10) [02:44:11 -117133.774940] SLOW spr round 12 (radius: 5) [02:46:52 -117133.408871] SLOW spr round 13 (radius: 5) [02:49:17 -117133.408832] SLOW spr round 14 (radius: 10) [02:51:54 -117133.408826] SLOW spr round 15 (radius: 15) [02:55:29] [worker #3] ML tree search #4, logLikelihood: -117160.329741 [02:56:33 -117133.408825] SLOW spr round 16 (radius: 20) [03:03:19 -117133.408825] SLOW spr round 17 (radius: 25) [03:12:01 -117133.408825] Model parameter optimization (eps = 0.100000) [03:12:09] [worker #0] ML tree search #5, logLikelihood: -117133.300437 [03:12:10 -302305.433347] Initial branch length optimization [03:12:14 -259081.733886] Model parameter optimization (eps = 10.000000) [03:13:04 -258724.747179] AUTODETECT spr round 1 (radius: 5) [03:15:19 -205595.686745] AUTODETECT spr round 2 (radius: 10) [03:17:55 -160287.434258] AUTODETECT spr round 3 (radius: 15) [03:18:35] [worker #1] ML tree search #6, logLikelihood: -117133.253034 [03:21:05 -139995.959003] AUTODETECT spr round 4 (radius: 20) [03:24:24 -133633.028199] AUTODETECT spr round 5 (radius: 25) [03:28:43 -130264.522004] SPR radius for FAST iterations: 25 (autodetect) [03:28:43 -130264.522004] Model parameter optimization (eps = 3.000000) [03:29:04 -130233.317786] FAST spr round 1 (radius: 25) [03:33:37 -118248.826636] FAST spr round 2 (radius: 25) [03:36:45 -117261.550264] FAST spr round 3 (radius: 25) [03:39:15 -117228.770214] FAST spr round 4 (radius: 25) [03:41:32 -117210.799089] FAST spr round 5 (radius: 25) [03:43:29 -117204.363959] FAST spr round 6 (radius: 25) [03:45:20 -117204.361370] Model parameter optimization (eps = 1.000000) [03:45:39 -117191.105312] SLOW spr round 1 (radius: 5) [03:48:10 -117156.731743] SLOW spr round 2 (radius: 5) [03:50:34 -117150.543830] SLOW spr round 3 (radius: 5) [03:52:52 -117150.541281] SLOW spr round 4 (radius: 10) [03:55:28 -117145.073268] SLOW spr round 5 (radius: 5) [03:58:17 -117137.801988] SLOW spr round 6 (radius: 5) [04:00:50 -117132.512170] SLOW spr round 7 (radius: 5) [04:03:12 -117132.402557] SLOW spr round 8 (radius: 5) [04:05:30 -117132.400385] SLOW spr round 9 (radius: 10) [04:08:04 -117130.232824] SLOW spr round 10 (radius: 5) [04:10:46 -117130.051429] SLOW spr round 11 (radius: 5) [04:13:13 -117130.051330] SLOW spr round 12 (radius: 10) [04:15:53 -117129.656738] SLOW spr round 13 (radius: 5) [04:18:33 -117129.650160] SLOW spr round 14 (radius: 10) [04:21:26 -117129.649018] SLOW spr round 15 (radius: 15) [04:26:04 -117129.648769] SLOW spr round 16 (radius: 20) [04:33:20 -117128.630175] SLOW spr round 17 (radius: 5) [04:36:11 -117128.626385] SLOW spr round 18 (radius: 10) [04:39:21 -117128.625088] SLOW spr round 19 (radius: 15) [04:43:58 -117128.624539] SLOW spr round 20 (radius: 20) [04:51:17 -117124.135798] SLOW spr round 21 (radius: 5) [04:54:10 -117124.132325] SLOW spr round 22 (radius: 10) [04:57:21 -117124.132120] SLOW spr round 23 (radius: 15) [05:01:58 -117124.132099] SLOW spr round 24 (radius: 20) [05:02:57] [worker #3] ML tree search #8, logLikelihood: -117121.531748 [05:06:27] [worker #2] ML tree search #7, logLikelihood: -117125.894861 [05:09:17 -117124.132087] SLOW spr round 25 (radius: 25) [05:18:33 -117123.562744] SLOW spr round 26 (radius: 5) [05:21:32 -117119.914763] SLOW spr round 27 (radius: 5) [05:24:05 -117119.914457] SLOW spr round 28 (radius: 10) [05:26:50 -117119.914441] SLOW spr round 29 (radius: 15) [05:31:27 -117119.914430] SLOW spr round 30 (radius: 20) [05:38:37 -117119.914420] SLOW spr round 31 (radius: 25) [05:42:24] [worker #1] ML tree search #10, logLikelihood: -117100.387245 [05:47:44 -117119.914409] Model parameter optimization (eps = 0.100000) [05:47:55] [worker #0] ML tree search #9, logLikelihood: -117119.795653 [05:47:55 -301094.525313] Initial branch length optimization [05:48:01 -258678.233518] Model parameter optimization (eps = 10.000000) [05:48:45 -258396.423025] AUTODETECT spr round 1 (radius: 5) [05:51:05 -207466.814595] AUTODETECT spr round 2 (radius: 10) [05:53:49 -161056.345457] AUTODETECT spr round 3 (radius: 15) [05:56:46 -141083.514866] AUTODETECT spr round 4 (radius: 20) [06:00:41 -131196.022564] AUTODETECT spr round 5 (radius: 25) [06:06:11 -128642.056908] SPR radius for FAST iterations: 25 (autodetect) [06:06:11 -128642.056908] Model parameter optimization (eps = 3.000000) [06:06:40 -128584.120184] FAST spr round 1 (radius: 25) [06:11:09 -117911.442050] FAST spr round 2 (radius: 25) [06:14:11 -117246.276459] FAST spr round 3 (radius: 25) [06:16:36 -117209.396968] FAST spr round 4 (radius: 25) [06:18:37 -117207.246114] FAST spr round 5 (radius: 25) [06:20:32 -117207.100625] FAST spr round 6 (radius: 25) [06:22:21 -117207.098840] Model parameter optimization (eps = 1.000000) [06:22:33 -117203.973488] SLOW spr round 1 (radius: 5) [06:25:03 -117155.320146] SLOW spr round 2 (radius: 5) [06:27:25 -117151.543698] SLOW spr round 3 (radius: 5) [06:29:46 -117151.190951] SLOW spr round 4 (radius: 5) [06:32:02 -117151.190761] SLOW spr round 5 (radius: 10) [06:34:36 -117148.294793] SLOW spr round 6 (radius: 5) [06:37:23 -117146.298179] SLOW spr round 7 (radius: 5) [06:39:52 -117146.194669] SLOW spr round 8 (radius: 5) [06:42:14 -117146.192484] SLOW spr round 9 (radius: 10) [06:44:50 -117141.884450] SLOW spr round 10 (radius: 5) [06:47:37 -117140.225560] SLOW spr round 11 (radius: 5) [06:50:05 -117140.111106] SLOW spr round 12 (radius: 5) [06:52:26 -117140.109481] SLOW spr round 13 (radius: 10) [06:55:03 -117137.474098] SLOW spr round 14 (radius: 5) [06:57:48 -117136.233178] SLOW spr round 15 (radius: 5) [07:00:15 -117136.224873] SLOW spr round 16 (radius: 10) [07:02:54 -117135.663504] SLOW spr round 17 (radius: 5) [07:05:34 -117135.613028] SLOW spr round 18 (radius: 10) [07:08:27 -117135.612909] SLOW spr round 19 (radius: 15) [07:12:54 -117135.612904] SLOW spr round 20 (radius: 20) [07:20:11 -117135.612904] SLOW spr round 21 (radius: 25) [07:29:46 -117135.612903] Model parameter optimization (eps = 0.100000) [07:30:00] [worker #0] ML tree search #13, logLikelihood: -117134.329893 [07:30:00 -304399.664004] Initial branch length optimization [07:30:05 -261269.059033] Model parameter optimization (eps = 10.000000) [07:30:42 -260921.861130] AUTODETECT spr round 1 (radius: 5) [07:33:01 -207096.606637] AUTODETECT spr round 2 (radius: 10) [07:35:49 -158450.587839] AUTODETECT spr round 3 (radius: 15) [07:38:53 -140159.838183] AUTODETECT spr round 4 (radius: 20) [07:39:22] [worker #2] ML tree search #11, logLikelihood: -117135.491369 [07:42:15 -133240.114831] AUTODETECT spr round 5 (radius: 25) [07:43:51] [worker #3] ML tree search #12, logLikelihood: -117152.965760 [07:46:45 -130045.236757] SPR radius for FAST iterations: 25 (autodetect) [07:46:45 -130045.236757] Model parameter optimization (eps = 3.000000) [07:47:07 -130011.208859] FAST spr round 1 (radius: 25) [07:51:28 -117836.036347] FAST spr round 2 (radius: 25) [07:54:38 -117249.426642] FAST spr round 3 (radius: 25) [07:57:14 -117173.493275] FAST spr round 4 (radius: 25) [07:59:27 -117162.910377] FAST spr round 5 (radius: 25) [08:01:24 -117160.001033] FAST spr round 6 (radius: 25) [08:03:14 -117159.998653] Model parameter optimization (eps = 1.000000) [08:03:25 -117158.217940] SLOW spr round 1 (radius: 5) [08:05:50 -117141.677769] SLOW spr round 2 (radius: 5) [08:08:11 -117138.274854] SLOW spr round 3 (radius: 5) [08:10:26 -117138.274286] SLOW spr round 4 (radius: 10) [08:12:58 -117137.910114] SLOW spr round 5 (radius: 5) [08:15:41 -117137.908397] SLOW spr round 6 (radius: 10) [08:18:36 -117137.549442] SLOW spr round 7 (radius: 5) [08:21:16 -117137.401234] SLOW spr round 8 (radius: 5) [08:23:41 -117137.360020] SLOW spr round 9 (radius: 10) [08:26:19 -117136.951278] SLOW spr round 10 (radius: 5) [08:29:01 -117136.945515] SLOW spr round 11 (radius: 10) [08:31:55 -117136.675751] SLOW spr round 12 (radius: 5) [08:34:34 -117136.674563] SLOW spr round 13 (radius: 10) [08:37:25 -117136.616695] SLOW spr round 14 (radius: 15) [08:42:11 -117132.079774] SLOW spr round 15 (radius: 5) [08:45:06 -117129.951531] SLOW spr round 16 (radius: 5) [08:47:38 -117129.221718] SLOW spr round 17 (radius: 5) [08:50:00 -117128.705934] SLOW spr round 18 (radius: 5) [08:52:17 -117128.705878] SLOW spr round 19 (radius: 10) [08:54:48 -117128.705871] SLOW spr round 20 (radius: 15) [08:59:39 -117128.173764] SLOW spr round 21 (radius: 5) [09:02:31 -117127.583879] SLOW spr round 22 (radius: 5) [09:05:02 -117127.319936] SLOW spr round 23 (radius: 5) [09:07:22 -117127.319858] SLOW spr round 24 (radius: 10) [09:09:56 -117127.319831] SLOW spr round 25 (radius: 15) [09:14:44 -117127.319818] SLOW spr round 26 (radius: 20) [09:17:02] [worker #1] ML tree search #14, logLikelihood: -117169.588288 [09:18:00] [worker #3] ML tree search #16, logLikelihood: -117123.578077 [09:21:47 -117127.319812] SLOW spr round 27 (radius: 25) [09:30:48 -117127.319808] Model parameter optimization (eps = 0.100000) [09:30:59] [worker #0] ML tree search #17, logLikelihood: -117126.914459 [10:22:47] [worker #2] ML tree search #15, logLikelihood: -117129.885979 [11:25:12] [worker #1] ML tree search #18, logLikelihood: -117094.150972 [12:46:31] [worker #3] ML tree search #20, logLikelihood: -117124.682534 [14:45:52] [worker #2] ML tree search #19, logLikelihood: -117099.726071 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.126845,0.177936) (0.082310,0.420480) (0.393667,0.891350) (0.397178,1.490327) 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: -117094.150972 AIC score: 237614.301944 / AICc score: 6109778.301944 / BIC score: 243229.712355 Free parameters (model + branch lengths): 1713 WARNING: Number of free parameters (K=1713) is larger than alignment size (n=196). 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/P20023/3_mltree/P20023.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/3_mltree/P20023.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/3_mltree/P20023.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P20023/3_mltree/P20023.raxml.log Analysis started: 04-Jul-2021 09:26:11 / finished: 05-Jul-2021 00:12:04 Elapsed time: 53152.807 seconds Consumed energy: 3170.620 Wh (= 16 km in an electric car, or 79 km with an e-scooter!)