richelbilderbeek
commented
5 years ago p230198@peregrine:beastier sbatch scripts/run_r_script scripts/issue_38.R
Submitted batch job 7443623
p230198@peregrine:beastier q
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
7443623 regular run_r_sc p230198 R 0:04 1 pg-node006
p230198@peregrine:beastier cat *.log
Rscript scripts/issue_38.R
[1] "input_filename: /home/p230198/.cache/filebd7e433f99c6/in_bd7e6acbcdd.xml"
[1] "output_log_filename: /home/p230198/.cache/filebd7e535e5387/out_bd7e6f726897.log"
[1] "output_trees_filenames: /home/p230198/.cache/filebd7e641e1863/out_bd7e4d3e6e43.trees"
[1] "output_state_filename: /home/p230198/.cache/filebd7e4dd8785/out_bd7e4093ba15.state.xml"
[1] ""
[2] " BEAST v2.6.0, 2002-2019"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Centre for Computational Evolution"
[8] " University of Auckland"
[9] " r.bouckaert@auckland.ac.nz"
[10] " alexei@cs.auckland.ac.nz"
[11] " "
[12] " Institute of Evolutionary Biology"
[13] " University of Edinburgh"
[14] " a.rambaut@ed.ac.uk"
[15] " "
[16] " David Geffen School of Medicine"
[17] " University of California, Los Angeles"
[18] " msuchard@ucla.edu"
[19] " "
[20] " Downloads, Help & Resources:"
[21] " http://beast2.org/"
[22] " "
[23] " Source code distributed under the GNU Lesser General Public License:"
[24] " http://github.com/CompEvol/beast2"
[25] " "
[26] " BEAST developers:"
[27] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
[30] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1566905272264"
[36] ""
[37] "File: in_bd7e6acbcdd.xml seed: 1566905272264 threads: 1"
[38] "Loading package NS v1.1.0"
[39] "Loading package MODEL_SELECTION v1.5.0"
[40] "Loading package BEAST v2.6.0"
[41] "Loading package BEASTLabs v1.9.0"
[42] "Loading package BEAST v2.6.0"
[43] "t1: 20 4"
[44] "t2: 20 4"
[45] "t3: 20 4"
[46] "t4: 20 4"
[47] "t5: 20 4"
[48] "Alignment(test_output_0)"
[49] " 5 taxa"
[50] " 20 sites"
[51] " 16 patterns"
[52] ""
[53] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
[54] "TreeLikelihood(treeLikelihood.test_output_00) uses BeerLikelihoodCore4"
[55] " Alignment(test_output_0): [taxa, patterns, sites] = [5, 16, 20]"
[56] "==============================================================================="
[57] "Citations for this model:"
[58] ""
[59] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[60] " Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "
[61] " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. "
[62] " PLoS computational biology 15, no. 4 (2019): e1006650."
[63] ""
[64] "==============================================================================="
[65] "Done!"
[1] "input_filename_full: /home/p230198/.cache/filebd7e433f99c6/in_bd7e6acbcdd.xml"
[1] "actual_log_filename: /home/p230198/.cache/filebd7e24cdd869/pff_bd7e1d065b91/test_output_0.log"
[1] "actual_trees_filenames: /home/p230198/.cache/filebd7e24cdd869/pff_bd7e1d065b91/test_output_0.trees"
[1] "output_log_filename_full: /home/p230198/.cache/filebd7e535e5387/out_bd7e6f726897.log"
[1] "output_trees_filenames_full: /home/p230198/.cache/filebd7e641e1863/out_bd7e4d3e6e43.trees"
[1] "output_state_filename_full: /home/p230198/.cache/filebd7e4dd8785/out_bd7e4093ba15.state.xml"
[1] ""
[2] " BEAST v2.6.0, 2002-2019"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Centre for Computational Evolution"
[8] " University of Auckland"
[9] " r.bouckaert@auckland.ac.nz"
[10] " alexei@cs.auckland.ac.nz"
[11] " "
[12] " Institute of Evolutionary Biology"
[13] " University of Edinburgh"
[14] " a.rambaut@ed.ac.uk"
[15] " "
[16] " David Geffen School of Medicine"
[17] " University of California, Los Angeles"
[18] " msuchard@ucla.edu"
[19] " "
[20] " Downloads, Help & Resources:"
[21] " http://beast2.org/"
[22] " "
[23] " Source code distributed under the GNU Lesser General Public License:"
[24] " http://github.com/CompEvol/beast2"
[25] " "
[26] " BEAST developers:"
[27] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
[30] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1566905275611"
[36] ""
[37] "File: in_bd7e6acbcdd.xml seed: 1566905275611 threads: 1"
[38] "Loading package NS v1.1.0"
[39] "Loading package MODEL_SELECTION v1.5.0"
[40] "Loading package BEAST v2.6.0"
[41] "Loading package BEASTLabs v1.9.0"
[42] "Loading package BEAST v2.6.0"
[43] "t1: 20 4"
[44] "t2: 20 4"
[45] "t3: 20 4"
[46] "t4: 20 4"
[47] "t5: 20 4"
[48] "Alignment(test_output_0)"
[49] " 5 taxa"
[50] " 20 sites"
[51] " 16 patterns"
[52] ""
[53] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
[54] "TreeLikelihood(treeLikelihood.test_output_00) uses BeerLikelihoodCore4"
[55] " Alignment(test_output_0): [taxa, patterns, sites] = [5, 16, 20]"
[56] "==============================================================================="
[57] "Citations for this model:"
[58] ""
[59] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[60] " Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "
[61] " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. "
[62] " PLoS computational biology 15, no. 4 (2019): e1006650."
[63] ""
[64] "==============================================================================="
[65] "Done!"
[1] "cmd: /home/p230198/.local/share/beast/bin/beast -statefile \"/home/p230198/.cache/filebd7e4dd8785/out_bd7e4093ba15.state.xml\" -overwrite \"/home/p230198/.cache/filebd7e433f99c6/in_bd7e6acbcdd.xml\""
[1] "[variable name]: [full path] [exists?]"
[1] "Filename: /home/p230198/.cache/filebd7e433f99c6/in_bd7e6acbcdd.xml TRUE"
[1] "input_filename_full: /home/p230198/.cache/filebd7e433f99c6/in_bd7e6acbcdd.xml"
[1] "actual_log_filename: /home/p230198/.cache/filebd7e24cdd869/pff_bd7e1d065b91/test_output_0.log FALSE"
[1] "actual_trees_filenames: /home/p230198/.cache/filebd7e24cdd869/pff_bd7e1d065b91/test_output_0.trees FALSE"
[1] "output_log_filename_full: /home/p230198/.cache/filebd7e535e5387/out_bd7e6f726897.log TRUE"
[1] "output_trees_filenames_full: /home/p230198/.cache/filebd7e641e1863/out_bd7e4d3e6e43.trees TRUE"
[1] "output_state_filename_full: /home/p230198/.cache/filebd7e4dd8785/out_bd7e4093ba15.state.xml TRUE"
[1] ""
[2] " BEAST v2.6.0, 2002-2019"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Centre for Computational Evolution"
[8] " University of Auckland"
[9] " r.bouckaert@auckland.ac.nz"
[10] " alexei@cs.auckland.ac.nz"
[11] " "
[12] " Institute of Evolutionary Biology"
[13] " University of Edinburgh"
[14] " a.rambaut@ed.ac.uk"
[15] " "
[16] " David Geffen School of Medicine"
[17] " University of California, Los Angeles"
[18] " msuchard@ucla.edu"
[19] " "
[20] " Downloads, Help & Resources:"
[21] " http://beast2.org/"
[22] " "
[23] " Source code distributed under the GNU Lesser General Public License:"
[24] " http://github.com/CompEvol/beast2"
[25] " "
[26] " BEAST developers:"
[27] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
[30] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Writing state to file /home/p230198/.cache/filebd7e4dd8785/out_bd7e4093ba15.state.xml"
[36] "Random number seed: 1566905277327"
[37] ""
[38] "File: in_bd7e6acbcdd.xml seed: 1566905277327 threads: 1"
[39] "Loading package NS v1.1.0"
[40] "Loading package MODEL_SELECTION v1.5.0"
[41] "Loading package BEAST v2.6.0"
[42] "Loading package BEASTLabs v1.9.0"
[43] "Loading package BEAST v2.6.0"
[44] "t1: 20 4"
[45] "t2: 20 4"
[46] "t3: 20 4"
[47] "t4: 20 4"
[48] "t5: 20 4"
[49] "Alignment(test_output_0)"
[50] " 5 taxa"
[51] " 20 sites"
[52] " 16 patterns"
[53] ""
[54] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
[55] "TreeLikelihood(treeLikelihood.test_output_00) uses BeerLikelihoodCore4"
[56] " Alignment(test_output_0): [taxa, patterns, sites] = [5, 16, 20]"
[57] "==============================================================================="
[58] "Citations for this model:"
[59] ""
[60] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[61] " Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "
[62] " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. "
[63] " PLoS computational biology 15, no. 4 (2019): e1006650."
[64] ""
[65] "==============================================================================="
[66] "Start likelihood: -106.32361113267788 "
[67] "Writing file test_output_0.log"
[68] "Writing file test_output_0.trees"
[69] " Sample posterior ESS(posterior) likelihood prior"
[70] " 0 -103.6475 N -99.3720 -4.2755 --"
[71] " 1000 -86.8988 2.0 -85.9742 -0.9245 --"
[72] " 2000 -87.1251 3.0 -85.0238 -2.1012 --"
[73] " 3000 -87.7236 4.0 -87.0724 -0.6511 --"
[74] ""
[75] "Operator Tuning #accept #reject Pr(m) Pr(acc|m)"
[76] "ScaleOperator(YuleBirthRateScaler.t:test_output_0) 0.75000 86 20 0.04000 0.81132 Try setting scaleFactor to about 0.562"
[77] "ScaleOperator(YuleModelTreeScaler.t:test_output_0) 0.50000 57 75 0.04000 0.43182 Try setting scaleFactor to about 0.278"
[78] "ScaleOperator(YuleModelTreeRootScaler.t:test_output_0) 0.50000 50 55 0.04000 0.47619 Try setting scaleFactor to about 0.25"
[79] "Uniform(YuleModelUniformOperator.t:test_output_0) - 554 643 0.40000 0.46282 "
[80] "SubtreeSlide(YuleModelSubtreeSlide.t:test_output_0) 1.00000 83 540 0.20000 0.13323 "
[81] "Exchange(YuleModelNarrow.t:test_output_0) - 154 437 0.20000 0.26058 "
[82] "Exchange(YuleModelWide.t:test_output_0) - 5 121 0.04000 0.03968 "
[83] "WilsonBalding(YuleModelWilsonBalding.t:test_output_0) - 3 118 0.04000 0.02479 "
[84] ""
[85] " Tuning: The value of the operator's tuning parameter, or '-' if the operator can't be optimized."
[86] " #accept: The total number of times a proposal by this operator has been accepted."
[87] " #reject: The total number of times a proposal by this operator has been rejected."
[88] " Pr(m): The probability this operator is chosen in a step of the MCMC (i.e. the normalized weight)."
[89] " Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator)."
[90] ""
[91] ""
[92] "Total calculation time: 0.449 seconds"
[93] "End likelihood: -87.72361632692947"
###############################################################################
Peregrine Cluster
Job 7443623 for user 'p230198'
Finished at: Tue Aug 27 13:27:59 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node006
Cores : 1
State : COMPLETED
Submit : 2019-08-27T13:27:41
Start : 2019-08-27T13:27:42
End : 2019-08-27T13:27:58
Reserved walltime : 10:00:00
Used walltime : 00:00:16
Used CPU time : 00:00:11 (efficiency: 73.84%)
% User (Computation): 85.31%
% System (I/O) : 14.69%
Mem reserved : 10G/node
Max Mem used : 0.00 (pg-node006)
Max Disk Write : 0.00 (pg-node006)
Max Disk Read : 0.00 (pg-node006)
Acknowledgements:
=================
Please see this page if you want to acknowledge Peregrine in your publications:
https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput
##################################################
There is evidence not any more