richelbilderbeek
commented
4 years ago Gotcha!
Closed richelbilderbeek closed 4 years ago
richelbilderbeek
commented
4 years ago Gotcha!
richelbilderbeek
commented
4 years ago Difference in storing/logging intervals in text:
as.character(
na.omit(
stringr::str_match(
string = readLines(beast2_options$input_filename),
pattern = ".*(store|log)Every.*"
)[, 1]
)
)gives:
[1] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"6000\" storeEvery=\"2000\">"
[2] " <state id=\"state\" storeEvery=\"5000\">"
[3] " <logger id=\"tracelog\" fileName=\"anthus_aco.log\" logEvery=\"2000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[4] " <logger id=\"screenlog\" logEvery=\"1000\">"
[5] " <logger id=\"treelog.t:anthus_aco\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">" Full file:
<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.4">
<data
id="anthus_aco"
name="alignment">
<sequence id="seq_61430_aco" taxon="61430_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagtcctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttgcagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctgccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_626029_aco" taxon="626029_aco" totalcount="4" value="acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtgtgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtacgtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggaaataatgtggatgttgtgtgtttaagcactgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagttaattttctgtacaagaaaattaagatcctactcagtgttcaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcattttatggaaacaaagttgggaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgctttacttagccatacctgtgagcntggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacccggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_630116_aco" taxon="630116_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagtcctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttgcagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctgccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_630210_aco" taxon="630210_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctcttagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaacaacatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtagttcnncangtnatttcttcacatcatttttaacctgcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctygtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaascatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_AMNH13589_aco" taxon="AMNH13589_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagtcctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttgcagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctgccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_B25702_aco" taxon="B25702_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcactttgtttggtggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggaaataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagttaattttctgtgcaagaaaattaagatcctactcaatgttcaggaaagtcaagaatattcctgtttttttctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagcttggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattcttgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_B41613_aco" taxon="B41613_aco" totalcount="4" value="acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggaaataatgtggatgttgtgtgtttaagcactgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagttaattttctgtacaagaaaattaagatcctactcagtgttcaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcattttatggaaacaaagttgggaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttcatagccatacctgtgagcntggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_B431_aco" taxon="B431_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcgaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacatttaattttctgtgcaagaaaattaacaacatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttcaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattagggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtattccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttaacattgattcaccagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccagccactctctgtttgtcttac"/>
<sequence id="seq_B48218_aco" taxon="B48218_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttattgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacttccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttataacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgtngcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattcttgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcancagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_B87109_aco" taxon="B87109_aco" totalcount="4" value="acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagatttttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggaaataatgtggatgttgtgtgtttaagcactgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagttaattttctgtgcaagaaaattaagatcctactcagtgttcaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttgggaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttcatagccatacctgtgagcntggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_FALK1_aco" taxon="FALK1_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagtcctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttgcagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctgccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_KU21673_aco" taxon="KU21673_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgggaagtcctttcagactgaaggatactctgatttttagctatggaaataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagttaattttctgtgcaagaaaattaagatcctactcagtgttcaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaaccaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagcttggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_KU25127_aco" taxon="KU25127_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacatttaattttctgtgcaagaaaattaacaacatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttcaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattagggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtattccttttcttctgctcttcccattctngtgtgtcttcaatagtttctgcaaataatgatgtgcagacttaacattgattcaccagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccagccactctctgtttgtcttac"/>
<sequence id="seq_KU3604_aco" taxon="KU3604_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccnagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcattttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtgaatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtcagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttctagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagcttgacagtgtctaaaattagaagtattccttttcttctgctcttcccattctagtgtgtcttcaatagtttctgcaaataatgatgtgcagacttaccattgattcaacagcagaggtaannatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_KU9813_aco" taxon="KU9813_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctcttagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaacaacatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtagttcnncangtnatttcttcacatcatttttaacctgcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_UWBM54394_aco" taxon="UWBM54394_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcgaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacatttaattttctgtgcaagaaaattaacaacatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattagggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtattccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaccagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccagccactctctgtttgtcttac"/>
<sequence id="seq_UWBM54511_aco" taxon="UWBM54511_aco" totalcount="4" value="acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggccaagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgagaagtcctttcagactgaaggatactctgaattttagctatggagataatgtggatgttgtgtgtttaagtcctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggacccttagaagccctcagtggcaaccacagagcgcacagttaattttctgtgcaagaaaattaagatcatactctgtgtccaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttgcagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctgccacttgaaaagacaaattaaaaacnaatttataatgcttatatgctttagttacattngggtctttcagtaactttagtgcttttgatagccatacctgtgagnttgacagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattgattcaacagcagaggtaagcatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_UWBM54556_aco" taxon="UWBM54556_aco" totalcount="4" value="acaggttagaaactactctgttttctggctgcttgtttaatgccctgtcctattttattgtgacaattgtctgtttttcacagaaaactgagagtagtcaagggattccttgtcctttgctttggtctgcacagctgtcttgttttaaggcccagtggaatgagacagctgactcttcaggtgtgaaaacttggatgtaggtgtagattggctctcagttgacctccagctggtgcagattcttcagtttgtttgatggagctttgggaagtcctttcagactgaaggatactctgatttttagctatggaaataatgtggatgttgtgtgtttaagccctgtttgcagtttttttctgttcagtcagttattttactgtgtgagtcaggactcttagaagccctctgtggcaaccacagagcgcatagtttattttctgtgcaagaaaattaagatcctactcagtgttcaggaaagtcaagaatattcctggttttctctactgtaaaattttatcttgtaacttgtgtttgggtctgcatgattattcaaaaatcttagtagatttggaaggatgttgcatattatggaaacaaagttggaaaaagtttgtatcagttccagtatttcttcacatcatttnttaacnncntnnnnnnnnngcttctaccacttgaaaagacaaattaaaaaccaatttataatgcttatatgctttagttacattngagtctttcagtaactttagtgcttttgatagccatacctgtgagcntggcagtgtctaaaattagaagtgttccttttcttctgctcttcccattctcgtgtgtcttcaatagtttctgcaaataatgatgtgcagacttagcattggttcaacagcagaggtaaaaatacctgtggcttacttggcttcagcttatccagcagtgccaaccactctctgtttgtcttac"/>
<sequence id="seq_bas3_aco" taxon="bas3_aco" totalcount="4" value="nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"/>
<sequence id="seq_chacoensis_aco" taxon="chacoensis_aco" totalcount="4" value="nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"/>
<sequence id="seq_dabbenei_aco" taxon="dabbenei_aco" totalcount="4" value="nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"/>
<sequence id="seq_meridae_aco" taxon="meridae_aco" totalcount="4" value="nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"/>
</data>
<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>
<run id="mcmc" spec="MCMC" chainLength="6000" storeEvery="2000">
<state id="state" storeEvery="5000">
<tree id="Tree.t:anthus_aco" name="stateNode">
<taxonset id="TaxonSet.anthus_aco" spec="TaxonSet">
<alignment idref="anthus_aco"/>
</taxonset>
</tree>
<parameter id="birthRate.t:anthus_aco" name="stateNode">1.0</parameter>
</state>
<init id="RandomTree.t:anthus_aco" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:anthus_aco" taxa="@anthus_aco">
<populationModel id="ConstantPopulation0.t:anthus_aco" spec="ConstantPopulation">
<parameter id="randomPopSize.t:anthus_aco" name="popSize">1.0</parameter>
</populationModel>
</init>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<distribution id="YuleModel.t:anthus_aco" spec="beast.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:anthus_aco" tree="@Tree.t:anthus_aco"/>
<prior id="YuleBirthRatePrior.t:anthus_aco" name="distribution" x="@birthRate.t:anthus_aco">
<Uniform id="Uniform.100" name="distr" upper="Infinity"/>
</prior>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
<distribution id="treeLikelihood.anthus_aco" spec="ThreadedTreeLikelihood" data="@anthus_aco" tree="@Tree.t:anthus_aco">
<siteModel id="SiteModel.s:anthus_aco" spec="SiteModel">
<parameter id="mutationRate.s:anthus_aco" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="gammaShape.s:anthus_aco" estimate="false" name="shape">1.0</parameter>
<parameter id="proportionInvariant.s:anthus_aco" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="JC69.s:anthus_aco" spec="JukesCantor"/>
</siteModel>
<branchRateModel id="StrictClock.c:anthus_aco" spec="beast.evolution.branchratemodel.StrictClockModel">
<parameter id="clockRate.c:anthus_aco" estimate="false" name="clock.rate">1.0</parameter>
</branchRateModel>
</distribution>
</distribution>
</distribution>
<operator id="YuleBirthRateScaler.t:anthus_aco" spec="ScaleOperator" parameter="@birthRate.t:anthus_aco" scaleFactor="0.75" weight="3.0"/>
<operator id="YuleModelTreeScaler.t:anthus_aco" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:anthus_aco" weight="3.0"/>
<operator id="YuleModelTreeRootScaler.t:anthus_aco" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:anthus_aco" weight="3.0"/>
<operator id="YuleModelUniformOperator.t:anthus_aco" spec="Uniform" tree="@Tree.t:anthus_aco" weight="30.0"/>
<operator id="YuleModelSubtreeSlide.t:anthus_aco" spec="SubtreeSlide" tree="@Tree.t:anthus_aco" weight="15.0"/>
<operator id="YuleModelNarrow.t:anthus_aco" spec="Exchange" tree="@Tree.t:anthus_aco" weight="15.0"/>
<operator id="YuleModelWide.t:anthus_aco" spec="Exchange" isNarrow="false" tree="@Tree.t:anthus_aco" weight="3.0"/>
<operator id="YuleModelWilsonBalding.t:anthus_aco" spec="WilsonBalding" tree="@Tree.t:anthus_aco" weight="3.0"/>
<logger id="tracelog" fileName="anthus_aco.log" logEvery="2000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.anthus_aco"/>
<log id="TreeHeight.t:anthus_aco" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:anthus_aco"/>
<log idref="YuleModel.t:anthus_aco"/>
<log idref="birthRate.t:anthus_aco"/>
</logger>
<logger id="screenlog" logEvery="1000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog.t:anthus_aco" fileName="$(tree).trees" logEvery="1000" mode="tree">
<log id="TreeWithMetaDataLogger.t:anthus_aco" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:anthus_aco"/>
</logger>
</run>
</beast>Fixed!
Bug is caused upstream:
The four estimates (at 0, 2, 4, 6k )is as expected, the seven phylogenies (at 0, 1, 2, 3, 4, 5, 6k) not.