CIPRES_THREADSPP=24 CIPRES_NP=1 running: modeltest-ng -p 24 -v-i infile.phy -t mp -o test1 -d aa -h u -m DAYHOFF, LG, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTRE, -r 12345 -u userfixedtree.tre _ _ _ _ _ _ _____ | | | | | | | | \ | |/ ____| _ __ ___ ___ __| | ___| | |_ ___ ___| |_ | \| | | __ | '_ ` _ \ / _ \ / _` |/ _ \ | __/ _ \/ __| __| | . ` | | |_ | | | | | | | (_) | (_| | __/ | || __/\__ \ |_ | |\ | |__| | |_| |_| |_|\___/ \__,_|\___|_|\__\___||___/\__| |_| \_|\_____| -------------------------------------------------------------------------------- modeltest-ng 0.1.5 Copyright (C) 2017 Diego Darriba, David Posada, Alexandros Stamatakis License GPLv3+: GNU GPL version 3 or later . This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by Diego Darriba. -------------------------------------------------------------------------------- Physical cores: 12 Logical cores: 24 Memory: 126GB Extensions: AVX [dbg] Create modeltest instance [dbg] Loading fixed tree from userfixedtree.tre [dbg] Ealuating checkpoint files Creating new checkpoint file: test1.ckp [dbg] New checkpoint file created -------------------------------------------------------------------------------- ModelTest-NG v0.1.5 Input data: MSA: infile.phy Tree: Fixed user file: userfixedtree.tre #taxa: 21 #sites: 113 #patterns: 111 Max. thread mem: 5 MB Output: Log: test1.log Results: test1.out Selection options: # protein matrices: 1 # protein models: 2 include model parameters: Uniform: true p-inv (+I): false gamma (+G): false both (+I+G): false free rates (+R): false fixed freqs: true estimated freqs: false asc bias: none epsilon (opt): 0.01 epsilon (par): 0.01 Additional options: verbosity: high threads: 24/12 RNG seed: 12345 subtree repeats: enabled -------------------------------------------------------------------------------- modeltest-ng was called as follows: >> modeltest-ng -p 24 -v -i infile.phy -t mp -o test1 -d aa -h u -m DAYHOFF, -r 12345 -u userfixedtree.tre LG, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTRE, Partition 1/1 [dbg] ... ... build partition optimizer [dbg] ... ... evaluate partition [dbg] Building parameters and computing initial lk score [dbg] Initial score: -3045.56 [dbg] Initial log likelihood: -3045.56 [dbg] final parameter optimization: -3045.56 [dbg] Building parameters and computing initial lk score [dbg] Initial score: -3029.88 [dbg] Initial log likelihood: -3029.88 [dbg] final parameter optimization: -3029.88 [dbg] fix branches -3042.79 [dbg] optimize BranchLengths: -3042.79 [dbg] optimize FixedFrequencies: -3042.79 [dbg] optimize Alpha: -3042.79 [dbg] optimize FixedSubstRates: -3042.79 [dbg] fix branches -3027.39 [dbg] optimize BranchLengths: -3027.39 [dbg] optimize FixedFrequencies: -3027.39 [dbg] optimize Alpha: -3027.39 [dbg] optimize FixedSubstRates: -3027.39 [dbg] fix branches -3042.79 [dbg] optimize BranchLengths: -3042.79 [dbg] optimize FixedFrequencies: -3042.79 [dbg] optimize Alpha: -3042.79 [dbg] optimize FixedSubstRates: -3042.79 [dbg] model done: [0.01/0.01]: -3042.79 [dbg] Model optimization done: -3042.79 3/2 DAYHOFF 0h:00:00 0h:00:00 -3042.7895 - - [dbg] fix branches -3027.39 [dbg] optimize BranchLengths: -3027.39 [dbg] optimize FixedFrequencies: -3027.39 [dbg] optimize Alpha: -3027.39 [dbg] optimize FixedSubstRates: -3027.39 [dbg] model done: [0.01/0.01]: -3027.39 [dbg] Model optimization done: -3027.39 2/2 DAYHOFF+F 0h:00:00 0h:00:00 -3027.3908 - - ----ID--- ----MODEL---- ---Time--- -Elapsed--- -------LnL------- -Alpha- -P-inv- Computation of likelihood scores completed. It took 0h:00:00 BIC model K lnL score delta weight -------------------------------------------------------------------------------- 1 DAYHOFF 0 -3042.7895 6269.9471 0.0000 1.0000 2 DAYHOFF+F 19 -3027.3908 6328.9701 59.0230 0.0000 -------------------------------------------------------------------------------- Best model according to BIC --------------------------- Model: DAYHOFF lnL: -3042.7895 Frequencies: 0.0871 0.0409 0.0404 0.0469 0.0335 0.0383 0.0495 0.0886 0.0336 0.0369 0.0854 0.0805 0.0148 0.0398 0.0507 0.0696 0.0585 0.0105 0.0299 0.0647 Inv. sites prop: - Gamma shape: - Score: 6269.9471 Weight: 1.0000 --------------------------- Parameter importances --------------------------- P.Inv: - Gamma: - Gamma-Inv: - Frequencies: 0.0000 --------------------------- Model averaged estimates --------------------------- P.Inv: - Alpha: - Alpha-P.Inv: - P.Inv-Alpha: - Frequencies: 0.0511 0.0873 0.0342 0.0608 0.0092 0.0207 0.0622 0.0907 0.0188 0.0743 0.0815 0.0781 0.0246 0.0704 0.0367 0.0420 0.0516 0.0058 0.0342 0.0656 Commands: > phyml -i infile.phy -d aa -m DAYHOFF -f m -v 0 -a 0 -c 1 -o tlr > raxmlHPC-SSE3 -s infile.phy -m PROTGAMMADAYHOFF -n EXEC_NAME -p PARSIMONY_SEED > raxml-ng --msa infile.phy --model DAYHOFF > paup -s infile.phy > iqtree -s infile.phy -m DAYHOFF AIC model K lnL score delta weight -------------------------------------------------------------------------------- 1 DAYHOFF 0 -3042.7895 6163.5789 0.0000 0.9734 2 DAYHOFF+F 19 -3027.3908 6170.7816 7.2026 0.0266 -------------------------------------------------------------------------------- Best model according to AIC --------------------------- Model: DAYHOFF lnL: -3042.7895 Frequencies: 0.0871 0.0409 0.0404 0.0469 0.0335 0.0383 0.0495 0.0886 0.0336 0.0369 0.0854 0.0805 0.0148 0.0398 0.0507 0.0696 0.0585 0.0105 0.0299 0.0647 Inv. sites prop: - Gamma shape: - Score: 6163.5789 Weight: 0.9734 --------------------------- Parameter importances --------------------------- P.Inv: - Gamma: - Gamma-Inv: - Frequencies: 0.0266 --------------------------- Model averaged estimates --------------------------- P.Inv: - Alpha: - Alpha-P.Inv: - P.Inv-Alpha: - Frequencies: 0.0511 0.0873 0.0342 0.0608 0.0092 0.0207 0.0622 0.0907 0.0188 0.0743 0.0815 0.0781 0.0246 0.0704 0.0367 0.0420 0.0516 0.0058 0.0342 0.0656 Commands: > phyml -i infile.phy -d aa -m DAYHOFF -f m -v 0 -a 0 -c 1 -o tlr > raxmlHPC-SSE3 -s infile.phy -m PROTGAMMADAYHOFF -n EXEC_NAME -p PARSIMONY_SEED > raxml-ng --msa infile.phy --model DAYHOFF > paup -s infile.phy > iqtree -s infile.phy -m DAYHOFF AICc model K lnL score delta weight -------------------------------------------------------------------------------- 1 DAYHOFF 0 -3042.7895 6205.5789 0.0000 1.0000 2 DAYHOFF+F 19 -3027.3908 6296.7816 91.2026 0.0000 -------------------------------------------------------------------------------- Best model according to AICc --------------------------- Model: DAYHOFF lnL: -3042.7895 Frequencies: 0.0871 0.0409 0.0404 0.0469 0.0335 0.0383 0.0495 0.0886 0.0336 0.0369 0.0854 0.0805 0.0148 0.0398 0.0507 0.0696 0.0585 0.0105 0.0299 0.0647 Inv. sites prop: - Gamma shape: - Score: 6205.5789 Weight: 1.0000 --------------------------- Parameter importances --------------------------- P.Inv: - Gamma: - Gamma-Inv: - Frequencies: 0.0000 --------------------------- Model averaged estimates --------------------------- P.Inv: - Alpha: - Alpha-P.Inv: - P.Inv-Alpha: - Frequencies: 0.0511 0.0873 0.0342 0.0608 0.0092 0.0207 0.0622 0.0907 0.0188 0.0743 0.0815 0.0781 0.0246 0.0704 0.0367 0.0420 0.0516 0.0058 0.0342 0.0656 Commands: > phyml -i infile.phy -d aa -m DAYHOFF -f m -v 0 -a 0 -c 1 -o tlr > raxmlHPC-SSE3 -s infile.phy -m PROTGAMMADAYHOFF -n EXEC_NAME -p PARSIMONY_SEED > raxml-ng --msa infile.phy --model DAYHOFF > paup -s infile.phy > iqtree -s infile.phy -m DAYHOFF Summary: Partition 1/1: Model Score Weight ---------------------------------------------------------- BIC DAYHOFF 6269.9471 1.0000 AIC DAYHOFF 6163.5789 0.9734 AICc DAYHOFF 6205.5789 1.0000 Execution results written to test1.out