richelbilderbeek
commented
6 years ago Closed richelbilderbeek closed 6 years ago
richelbilderbeek
commented
6 years ago richelbilderbeek
commented
6 years ago Clearer one:
p230198@peregrine:scripts cat test_random_1_698487.log
slurmstepd: error: Unable to create TMPDIR [/local/698471]: Permission denied
slurmstepd: error: Setting TMPDIR to /tmp
The following have been reloaded with a version change:
1) ncurses/6.0 => ncurses/6.0-foss-2016a
[1] "seed: 1720802175"
[1] 1
...
[1] 80
[1] "ERROR"
[1] ""
[2] " BEAST v2.4.0, 2002-2016"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Department of Computer Science"
[8] " University of Auckland"
[9] " remco@cs.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, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1519992095127"
[36] ""
[37] "Loading package BEAST v2.4.0"
[38] "61430_aco: 960 4"
[39] "626029_aco: 960 4"
[40] "630116_aco: 960 4"
[41] "630210_aco: 960 4"
[42] "AMNH13589_aco: 960 4"
[43] "B25702_aco: 960 4"
[44] "B41613_aco: 960 4"
[45] "B431_aco: 960 4"
[46] "B48218_aco: 960 4"
[47] "B87109_aco: 960 4"
[48] "FALK1_aco: 960 4"
[49] "KU21673_aco: 960 4"
[50] "KU25127_aco: 960 4"
[51] "KU3604_aco: 960 4"
[52] "KU9813_aco: 960 4"
[53] "UWBM54394_aco: 960 4"
[54] "UWBM54511_aco: 960 4"
[55] "UWBM54556_aco: 960 4"
[56] "bas3_aco: 960 4"
[57] "chacoensis_aco: 960 4"
[58] "dabbenei_aco: 960 4"
[59] "meridae_aco: 960 4"
[60] "Alignment(anthus_aco)"
[61] " 22 taxa"
[62] " 960 sites"
[63] " 70 patterns"
[64] ""
[65] ""
[66] "Error 110 parsing the xml input file"
[67] ""
[68] "nullvalidate and intialize error: Cannot compute beta density at 1 when beta = %.3g"
[69] ""
[70] "Error detected about here:"
[71] " <beast>"
[72] " <run id='mcmc' spec='MCMC'>"
[73] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[74] " <distribution id='prior' spec='util.CompoundDistribution'>"
[75] " <prior id='YuleBirthRatePrior.t:anthus_aco' name='distribution'>"
[76] ""
attr(,"status")
[1] 1
[1] "site model:"
$name
[1] "TN93"
$id
[1] NA
$gamma_site_model
$gamma_site_model$gamma_cat_count
[1] 4
$gamma_site_model$gamma_shape
[1] 0.7302075
$gamma_site_model$prop_invariant
[1] 0.1680064
$gamma_site_model$gamma_shape_prior_distr
$gamma_site_model$gamma_shape_prior_distr$name
[1] "normal"
$gamma_site_model$gamma_shape_prior_distr$id
[1] NA
$gamma_site_model$gamma_shape_prior_distr$mean
$gamma_site_model$gamma_shape_prior_distr$mean$name
[1] "mean"
$gamma_site_model$gamma_shape_prior_distr$mean$id
[1] NA
$gamma_site_model$gamma_shape_prior_distr$mean$estimate
[1] TRUE
$gamma_site_model$gamma_shape_prior_distr$mean$value
[1] -54.18868
$gamma_site_model$gamma_shape_prior_distr$sigma
$gamma_site_model$gamma_shape_prior_distr$sigma$name
[1] "sigma"
$gamma_site_model$gamma_shape_prior_distr$sigma$id
[1] NA
$gamma_site_model$gamma_shape_prior_distr$sigma$estimate
[1] TRUE
$gamma_site_model$gamma_shape_prior_distr$sigma$value
[1] 87.09289
$kappa_1_prior_distr
$kappa_1_prior_distr$name
[1] "inv_gamma"
$kappa_1_prior_distr$id
[1] NA
$kappa_1_prior_distr$alpha
$kappa_1_prior_distr$alpha$name
[1] "alpha"
$kappa_1_prior_distr$alpha$id
[1] NA
$kappa_1_prior_distr$alpha$estimate
[1] TRUE
$kappa_1_prior_distr$alpha$value
[1] 84.64905
$kappa_1_prior_distr$beta
$kappa_1_prior_distr$beta$name
[1] "beta"
$kappa_1_prior_distr$beta$id
[1] NA
$kappa_1_prior_distr$beta$estimate
[1] FALSE
$kappa_1_prior_distr$beta$value
[1] 97.37161
$kappa_2_prior_distr
$kappa_2_prior_distr$name
[1] "one_div_x"
$kappa_2_prior_distr$id
[1] NA
$kappa_1_param
$kappa_1_param$name
[1] "kappa_1"
$kappa_1_param$id
[1] NA
$kappa_1_param$lower
[1] -37.24834
$kappa_1_param$value
[1] -2.776015
$kappa_2_param
$kappa_2_param$name
[1] "kappa_2"
$kappa_2_param$id
[1] NA
$kappa_2_param$lower
[1] -1.522128
$kappa_2_param$value
[1] 63.64398
$freq_equilibrium
[1] "all_equal"
[1] "clock model:"
$name
[1] "strict"
$id
[1] NA
$clock_rate_param
$clock_rate_param$name
[1] "clock_rate"
$clock_rate_param$id
[1] NA
$clock_rate_param$estimate
[1] TRUE
$clock_rate_param$value
[1] -30.73944
$clock_rate_distr
$clock_rate_distr$name
[1] "beta"
$clock_rate_distr$id
[1] NA
$clock_rate_distr$alpha
$clock_rate_distr$alpha$name
[1] "alpha"
$clock_rate_distr$alpha$id
[1] NA
$clock_rate_distr$alpha$estimate
[1] FALSE
$clock_rate_distr$alpha$value
[1] 2.307688
$clock_rate_distr$beta
$clock_rate_distr$beta$name
[1] "beta"
$clock_rate_distr$beta$id
[1] NA
$clock_rate_distr$beta$estimate
[1] FALSE
$clock_rate_distr$beta$value
[1] 29.403
[1] "tree prior:"
$name
[1] "yule"
$id
[1] NA
$birth_rate_distr
$birth_rate_distr$name
[1] "beta"
$birth_rate_distr$id
[1] NA
$birth_rate_distr$alpha
$birth_rate_distr$alpha$name
[1] "alpha"
$birth_rate_distr$alpha$id
[1] NA
$birth_rate_distr$alpha$estimate
[1] TRUE
$birth_rate_distr$alpha$value
[1] 10.19581
$birth_rate_distr$beta
$birth_rate_distr$beta$name
[1] "beta"
$birth_rate_distr$beta$id
[1] NA
$birth_rate_distr$beta$estimate
[1] TRUE
$birth_rate_distr$beta$value
[1] 0.5531086
[1] "seed: 1720802175"
Warning messages:
1: running command 'java -jar ~/Programs/beast/lib/beast.jar -validate /local/698487/RtmpBLt8am/file671b4f7be367 2>/dev/null' had status 1
2: In file.create(to[okay]) :
cannot create file '/home/richel/bad.xml', reason 'No such file or directory'
3: running command 'java -jar ~/Programs/beast/lib/beast.jar -validate /local/698487/RtmpBLt8am/file671b4f7be367 2>/dev/null' had status 1 Another one:
p230198@peregrine:scripts cat test_random_1_698477.log
The following have been reloaded with a version change:
1) ncurses/6.0 => ncurses/6.0-foss-2016a
[1] "seed: 1720903633"
[1] 1
...
[1] 262
[1] "ERROR"
[1] ""
[2] " BEAST v2.4.0, 2002-2016"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Department of Computer Science"
[8] " University of Auckland"
[9] " remco@cs.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, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1519992789499"
[36] ""
[37] "Loading package BEAST v2.4.0"
[38] "61430_aco: 960 4"
[39] "626029_aco: 960 4"
[40] "630116_aco: 960 4"
[41] "630210_aco: 960 4"
[42] "AMNH13589_aco: 960 4"
[43] "B25702_aco: 960 4"
[44] "B41613_aco: 960 4"
[45] "B431_aco: 960 4"
[46] "B48218_aco: 960 4"
[47] "B87109_aco: 960 4"
[48] "FALK1_aco: 960 4"
[49] "KU21673_aco: 960 4"
[50] "KU25127_aco: 960 4"
[51] "KU3604_aco: 960 4"
[52] "KU9813_aco: 960 4"
[53] "UWBM54394_aco: 960 4"
[54] "UWBM54511_aco: 960 4"
[55] "UWBM54556_aco: 960 4"
[56] "bas3_aco: 960 4"
[57] "chacoensis_aco: 960 4"
[58] "dabbenei_aco: 960 4"
[59] "meridae_aco: 960 4"
[60] "Alignment(anthus_aco)"
[61] " 22 taxa"
[62] " 960 sites"
[63] " 70 patterns"
[64] ""
[65] ""
[66] "Error 110 parsing the xml input file"
[67] ""
[68] "nullvalidate and intialize error: Cannot compute beta density at 1 when beta = %.3g"
[69] ""
[70] "Error detected about here:"
[71] " <beast>"
[72] " <run id='mcmc' spec='MCMC'>"
[73] " <distribution id='posterior' spec='util.CompoundDistribution'>"
[74] " <distribution id='prior' spec='util.CompoundDistribution'>"
[75] " <prior id='YuleBirthRatePrior.t:anthus_aco' name='distribution'>"
[76] ""
attr(,"status")
[1] 1
[1] "site model:"
$name
[1] "JC69"
$id
[1] NA
$gamma_site_model
$gamma_site_model$gamma_cat_count
[1] 1
$gamma_site_model$gamma_shape
[1] 0.9731957
$gamma_site_model$prop_invariant
[1] 0.9324796
$gamma_site_model$gamma_shape_prior_distr
$gamma_site_model$gamma_shape_prior_distr$name
[1] "exponential"
$gamma_site_model$gamma_shape_prior_distr$id
[1] NA
$gamma_site_model$gamma_shape_prior_distr$mean
$gamma_site_model$gamma_shape_prior_distr$mean$name
[1] "mean"
$gamma_site_model$gamma_shape_prior_distr$mean$id
[1] NA
$gamma_site_model$gamma_shape_prior_distr$mean$estimate
[1] FALSE
$gamma_site_model$gamma_shape_prior_distr$mean$value
[1] -38.87837
[1] "clock model:"
$name
[1] "strict"
$id
[1] NA
$clock_rate_param
$clock_rate_param$name
[1] "clock_rate"
$clock_rate_param$id
[1] NA
$clock_rate_param$estimate
[1] FALSE
$clock_rate_param$value
[1] 65.35282
$clock_rate_distr
$clock_rate_distr$name
[1] "exponential"
$clock_rate_distr$id
[1] NA
$clock_rate_distr$mean
$clock_rate_distr$mean$name
[1] "mean"
$clock_rate_distr$mean$id
[1] NA
$clock_rate_distr$mean$estimate
[1] TRUE
$clock_rate_distr$mean$value
[1] -72.34374
[1] "tree prior:"
$name
[1] "yule"
$id
[1] NA
$birth_rate_distr
$birth_rate_distr$name
[1] "beta"
$birth_rate_distr$id
[1] NA
$birth_rate_distr$alpha
$birth_rate_distr$alpha$name
[1] "alpha"
$birth_rate_distr$alpha$id
[1] NA
$birth_rate_distr$alpha$estimate
[1] FALSE
$birth_rate_distr$alpha$value
[1] 92.56053
$birth_rate_distr$beta
$birth_rate_distr$beta$name
[1] "beta"
$birth_rate_distr$beta$id
[1] NA
$birth_rate_distr$beta$estimate
[1] FALSE
$birth_rate_distr$beta$value
[1] 0.6195184
[1] "seed: 1720903633"Found from BEAST2 source code:
if (beta < 1) {
throw MathRuntimeException.createIllegalArgumentException(
"Cannot compute beta density at 1 when beta = %.3g", beta);
}Indeed, in all cases beta was below 1.0.
richelbilderbeek
commented
6 years ago 'Beta distribution must have a beta value of at least 1.0'