richelbilderbeek
commented
5 years ago Yup, babette works on Peregrine.
p230198@peregrine:babette sbatch scripts/run_r_script scripts/issue_70.R
Submitted batch job 7443715
p230198@peregrine:babette q
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
7443715 regular run_r_sc p230198 PD 0:00 1 (None)
p230198@peregrine:babette cat *.log
Rscript scripts/issue_70.R
[1] "input_filename: /home/p230198/.cache/file24b013c533c71/in_24b0150e7dc28.xml"
[1] "output_log_filename: /home/p230198/.cache/file24b015389689c/out_24b01a49955f.log"
[1] "output_trees_filenames: /home/p230198/.cache/file24b014f9e2e66/out_24b0179b85023.trees"
[1] "output_state_filename: /home/p230198/.cache/file24b017849c266/out_24b01471a9a7b.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: 1566906712686"
[36] ""
[37] "File: in_24b0150e7dc28.xml seed: 1566906712686 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/file24b013c533c71/in_24b0150e7dc28.xml"
[1] "actual_log_filename: /home/p230198/.cache/file24b017f6b9cf9/pff_24b0111b3abe4/test_output_0.log"
[1] "actual_trees_filenames: /home/p230198/.cache/file24b017f6b9cf9/pff_24b0111b3abe4/test_output_0.trees"
[1] "output_log_filename_full: /home/p230198/.cache/file24b015389689c/out_24b01a49955f.log"
[1] "output_trees_filenames_full: /home/p230198/.cache/file24b014f9e2e66/out_24b0179b85023.trees"
[1] "output_state_filename_full: /home/p230198/.cache/file24b017849c266/out_24b01471a9a7b.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: 1566906715269"
[36] ""
[37] "File: in_24b0150e7dc28.xml seed: 1566906715269 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/file24b017849c266/out_24b01471a9a7b.state.xml\" -overwrite \"/home/p230198/.cache/file24b013c533c71/in_24b0150e7dc28.xml\""
[1] "[variable name]: [full path] [exists?]"
[1] "Filename: /home/p230198/.cache/file24b013c533c71/in_24b0150e7dc28.xml TRUE"
[1] "input_filename_full: /home/p230198/.cache/file24b013c533c71/in_24b0150e7dc28.xml"
[1] "actual_log_filename: /home/p230198/.cache/file24b017f6b9cf9/pff_24b0111b3abe4/test_output_0.log FALSE"
[1] "actual_trees_filenames: /home/p230198/.cache/file24b017f6b9cf9/pff_24b0111b3abe4/test_output_0.trees FALSE"
[1] "output_log_filename_full: /home/p230198/.cache/file24b015389689c/out_24b01a49955f.log TRUE"
[1] "output_trees_filenames_full: /home/p230198/.cache/file24b014f9e2e66/out_24b0179b85023.trees TRUE"
[1] "output_state_filename_full: /home/p230198/.cache/file24b017849c266/out_24b01471a9a7b.state.xml TRUE"
$test_output_0_trees
4 phylogenetic trees
$estimates
Sample posterior likelihood prior treeLikelihood TreeHeight YuleModel
1 0 -134.80849 -130.08066 -4.7278332 -130.08066 1.7475369 -4.7278332
2 1000 -86.47299 -86.15352 -0.3194761 -86.15352 0.6109851 -0.3194761
3 2000 -88.28232 -85.60606 -2.6762592 -85.60606 1.2095052 -2.6762592
4 3000 -88.96634 -89.34677 0.3804330 -89.34677 0.4775564 0.3804330
birthRate
1 1.000000
2 4.197404
3 1.036608
4 2.219897
$operators
operator p accept reject acceptFC rejectFC rejectIv
1 YuleBirthRateScaler.t 0.75 116 14 0 0 0
2 YuleModelTreeScaler.t 0.50 48 50 0 0 0
3 YuleModelTreeRootScaler.t 0.50 54 63 0 0 0
4 YuleModelUniformOperator.t NaN 596 639 0 0 0
5 YuleModelSubtreeSlide.t 1.00 73 517 0 0 220
6 YuleModelNarrow.t NaN 118 448 0 0 0
7 YuleModelWide.t NaN 3 134 0 0 83
8 YuleModelWilsonBalding.t NaN 6 122 0 0 71
rejectOp
1 0
2 0
3 0
4 0
5 220
6 0
7 83
8 71
$output
[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/file24b017849c266/out_24b01471a9a7b.state.xml"
[36] "Random number seed: 1566906716912"
[37] ""
[38] "File: in_24b0150e7dc28.xml seed: 1566906716912 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: -134.80849467219977 "
[67] "Writing file test_output_0.log"
[68] "Writing file test_output_0.trees"
[69] " Sample posterior ESS(posterior) likelihood prior"
[70] " 0 -134.8084 N -130.0806 -4.7278 --"
[71] " 1000 -86.4729 2.0 -86.1535 -0.3194 --"
[72] " 2000 -88.2823 3.0 -85.6060 -2.6762 --"
[73] " 3000 -88.9663 4.0 -89.3467 0.3804 --"
[74] ""
[75] "Operator Tuning #accept #reject Pr(m) Pr(acc|m)"
[76] "ScaleOperator(YuleBirthRateScaler.t:test_output_0) 0.75000 116 14 0.04000 0.89231 Try setting scaleFactor to about 0.562"
[77] "ScaleOperator(YuleModelTreeScaler.t:test_output_0) 0.50000 48 50 0.04000 0.48980 Try setting scaleFactor to about 0.25"
[78] "ScaleOperator(YuleModelTreeRootScaler.t:test_output_0) 0.50000 54 63 0.04000 0.46154 Try setting scaleFactor to about 0.255"
[79] "Uniform(YuleModelUniformOperator.t:test_output_0) - 596 639 0.40000 0.48259 "
[80] "SubtreeSlide(YuleModelSubtreeSlide.t:test_output_0) 1.00000 73 517 0.20000 0.12373 "
[81] "Exchange(YuleModelNarrow.t:test_output_0) - 118 448 0.20000 0.20848 "
[82] "Exchange(YuleModelWide.t:test_output_0) - 3 134 0.04000 0.02190 "
[83] "WilsonBalding(YuleModelWilsonBalding.t:test_output_0) - 6 122 0.04000 0.04688 "
[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: 0.452 seconds"
[93] "End likelihood: -88.96634057506891"
###############################################################################
Peregrine Cluster
Job 7443715 for user 'p230198'
Finished at: Tue Aug 27 13:51:58 CEST 2019
Job details:
============
Name : run_r_script
User : p230198
Partition : regular
Nodes : pg-node021
Cores : 1
State : COMPLETED
Submit : 2019-08-27T13:51:40
Start : 2019-08-27T13:51:41
End : 2019-08-27T13:51:58
Reserved walltime : 10:00:00
Used walltime : 00:00:17
Used CPU time : 00:00:11 (efficiency: 66.74%)
% User (Computation): 85.65%
% System (I/O) : 14.34%
Mem reserved : 10G/node
Max Mem used : 0.00 (pg-node021)
Max Disk Write : 0.00 (pg-node021)
Max Disk Read : 0.00 (pg-node021)
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 against this