create_beast2_input_file() ignores tipdates_filename argument

[WJH58]

Describe the bug
Whatever tipdates filename I specify or even when the tipdates file does not exist, create_beast2_input_file() keeps running smoothly and generate a xml file that does not contain any tip dates information.

To Reproduce

## generate beast2 input xml file with tip dates 
create_beast2_input_file(
    fasta_filename,
    output_filename,
    tipdates_filename = "temp_date.txt",
    clock_model = create_rln_clock_model(),
    site_model = create_gtr_site_model(),
    mcmc = create_mcmc(),
    tree_prior = create_cbs_tree_prior(),
    beauti_options = create_beauti_options_v2_6()
)
run_beast2(
  input_filename = output_filename,
  output_state_filename = create_temp_state_filename(),
  use_beagle = TRUE
)

## treeannotator
cmd <- glue("treeannotator -burnin 1000 -heights mean test.trees test.nex")
system(cmd)

## ggtree plot time-scaled tree
tree <- read.beast('test.nex')
ggtree(tree, mrsd = "2013-01-01") + theme_tree2()

Expected behavior

1. I hope when my tip dates file format is not accepted or when the file path does not exist, the function create_beast2_input_file() would report error and stop.
2. I hope the output xml file would contain tip dates value. Otherwise run_beast2() does not produce time-scaled trees and ggtree does not plot correct ladder-like time-scaled tree.

Screenshots

My files if you would like to test

## This is my temp_date.txt. The dates are written in decimal numeric format. 
##Apart from decimal dates, I tried "m%-d%-Y%" in the 2nd column as well but create_beast2_input_file() simply ignores the tipdates_filename argument.

A/Goose/Guangdong/1/1996_H5N1_EPI_ISL_1254_0	1996.5
A/Environment/Hong_Kong/437-4/1999_H5N1_EPI_ISL_1459_0	1999.5
A/Environment/Hong_Kong/437-6/1999_H5N1_EPI_ISL_1460_0	1999.5
A/Environment/Hong_Kong/437-8/1999_H5N1_EPI_ISL_1461_0	1999.5
A/Environment/Hong_Kong/437-10/1999_H5N1_EPI_ISL_1462_0	1999.5
A/goose/Guangdong/3/1997_H5N1_EPI_ISL_1909_0	1997.5
A/chicken/Hubei/wh/1997_H5N1_EPI_ISL_68662_0	1997.5
A/chicken/Hubei/wj/1997_H5N1_EPI_ISL_68664_0	1997.5
A/chicken/Hubei/wl/1997_H5N1_EPI_ISL_68666_0	1997.5
A/duck/Guangxi/07/1999_H5N1_EPI_ISL_3895_0	1999.5
A/goose/Guangdong/1/1996-01-01_H5N1_EPI_ISL_17767104_0	1996

## This is my fasta file.
>A/Goose/Guangdong/1/1996_H5N1_EPI_ISL_1254_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACTT
ACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAATTTAAACAAGCAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/goose/Guangdong/1/1996-01-01_H5N1_EPI_ISL_17767104_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACTT
ACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAATTTAAACAAGCAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/goose/Guangdong/3/1997_H5N1_EPI_ISL_1909_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACTT
ACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCGCCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACCCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAATTTAAACAAGCAGATGGAAGACGGACTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/Environment/Hong_Kong/437-4/1999_H5N1_EPI_ISL_1459_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAATAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACAACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAAGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ATATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGGGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGGAT
AGAAAATTTGAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGCCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/Environment/Hong_Kong/437-10/1999_H5N1_EPI_ISL_1462_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAATAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACAACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAAGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTACCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ATATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGGGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGGAT
AGAAAATTTGAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/Environment/Hong_Kong/437-6/1999_H5N1_EPI_ISL_1460_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACAACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAAGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ATATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGGAT
AGAAAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAGCAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/Environment/Hong_Kong/437-8/1999_H5N1_EPI_ISL_1461_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAATAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
TCCAGGGGATTTCAACAACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAAGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ATATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTGAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCC
AAATATGTGGAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGGGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGGAT
AGAAAATTTGAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGGAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/chicken/Hubei/wl/1997_H5N1_EPI_ISL_68666_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGAAACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAATTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTAGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCGCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAAAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGCGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGCGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAGTTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/chicken/Hubei/wj/1997_H5N1_EPI_ISL_68664_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCACCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ATATTTCCGTTGGGACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAAAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGAGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGATAGAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAGTTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGTACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/chicken/Hubei/wh/1997_H5N1_EPI_ISL_68662_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACA
ACGGGAAGCTCTGCGATCTAGATGGAGTAAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAC
CCTATGTGTGACGAATTCACCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTA
CCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAGTTCTTGGTCCGATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCCACAATAAAGAGGAGCTACAATAATACCAACCAAGA
AGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACATTTTTAAAGCCGAATGATGCCATCAATTTCGAAAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCA
AGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAGA---------AGAAG
AAAAAAGCGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGCGGATACGCTGCAGACAAAGAATCCACTCCAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGAT
AGAGAGTTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAA
ATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTA
TGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT
>A/duck/Guangxi/07/1999_H5N1_EPI_ISL_3895_0
ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTGAAAGTGATCAAATTTGCATTGGTTACCATGCAAACAA
CTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACA
ACGGGAAGCTCTGCAATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAAT
CCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCTAGCCCAGCCAATGACCTCTGTTA
CCCAGGGGATCTCAATGACTATGAAGAACTGAAACACCTATTGAGCAGCACAAACCATTTTGAGAAAATTCAGATCATCC
CCAAAAATTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA---TGTCCATACCATGGGAGGTCCTCCTTT
TTCAGAAATGTGGTATGGCTTACCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCCAGA
AGATCTTTTGATACTGTGGGGGATTCACCATCCTAATGATGCAGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCT
ACGTTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGT
GGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCC
AGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATAGTAACTGCAACACCA
AGTGTCAAACTCCAATAGGGGCGATAAACTCTAGTATGCCATTCCACAACATACATCCTCTCACCATCGGGGAATGCCCC
AAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAAAGAGAGAAA---------AGAAG
AAAAAAGAGAGGGCTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGT
ACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAAT
AAGGTCAATTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGAAT
AGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAGA
ATGAGAGAACTCTATACTTTCATGACTCAAATGTCAAGGACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCA
AAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTA
TGACTATCCGCAGTATTCAGAAGAAGCAAGGCTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTT
ACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGG
ATGTGCTCCAATGGATCATTACAATGCAGAATTTGCATT

[richelbilderbeek]

Thanks for this bug report! I will take a look now ...

[richelbilderbeek]

Note to self:

Indeed, creating the BEAST2 input file works perfect:

test_that("use", {
  expect_true(file.exists(get_beautier_path("babette_issue_108_tipdates.txt")))
  expect_true(file.exists(get_beautier_path("babette_issue_108.fasta")))
  fasta_filename <- get_beautier_path("babette_issue_108.fasta")
  output_filename <- get_beautier_tempfilename()
  tipdates_filename <- get_beautier_tempfilename(pattern = "absent_")
  create_beast2_input_file(
    fasta_filename,
    output_filename,
    tipdates_filename = tipdates_filename,
    clock_model = create_rln_clock_model(),
    site_model = create_gtr_site_model(),
    mcmc = create_mcmc(),
    tree_prior = create_cbs_tree_prior(),
    beauti_options = create_beauti_options_v2_6()
  )
  expect_true(file.exists(output_filename))
  expect_false(file.exists(tipdates_filename))
  remove_beautier_folder()
})

This test is in beautier, on the develop branch 👍

[richelbilderbeek]

Note to self:

• [FALSE] It is a feature of beautier/babette to not check if the tipdates file is present yes/no at the time before running
• [FALSE] it seems that BEAST2 does not give the expected error when this file is absent

/usr/lib/jvm/java-21-openjdk-amd64/bin/java -cp /home/richel/.local/share/beast/lib/launcher.jar beast.app.beastapp.BeastLauncher -statefile /home/richel/.cache/beastier/beast2_29dcf25ef0351b.xml.state -overwrite ~/.cache/beautier/file29dcf22ec106cc

Attaching the created XML...
babette_issue_108.zip

[richelbilderbeek]

Note to self:

On the other hand, it seems that the absent tipdates file did not make it into the XML at all ...?

[richelbilderbeek]

Note to self: the tipdates file is not stored in the BEAST2 input XML file. Instead, its content is added to the sequences, e.g.

GAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGT---CTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATT"/>
                                
        <sequence id="seq_A/goose/Guangdong/3/1997_H5N1_EPI_ISL_1909_0" spec="Sequence" taxon="A/goose/Guangdong/3/1997_H5N1_EPI_ISL_1909_0" totalcount="4" value="ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGA

So indeed beautier should give an error!

[richelbilderbeek]

Hi @WJH58,

Thanks again for this bug report! I think I fixed it. To use the new code, install it with:

remotes::install_github("ropensci/beautier", ref = "develop")

Could you confirm that now you get a proper error message?

I've added you as a contributor of the beautier package as I know how tedious it is to make a proper bug report like that 👍

[richelbilderbeek]

P.S. the code will reach CRAN when testing has finished and after CRAN has had their (well-deserved) holidays 👍

[WJH58]

@richelbilderbeek
Thanks for your quick reply! I've installed the developed version and tried again, and indeed the function check_inference_model would check whether the tip dates file exists. However, the produced xml file still does not contain tip dates information:

 <state id="state" spec="State" storeEvery="5000">
            <tree id="Tree.t:2006-2007" spec="beast.evolution.tree.Tree" name="stateNode">
                <trait id="dateTrait.t:2006-2007" spec="beast.evolution.tree.TraitSet" traitname="date" value="">   ## value is empty!

[WJH58]

It is because of the function tipdate_taxa_to_xml_trait():

function (inference_model) 
{
    id <- inference_model$tree_prior$id
    trait_set_str <- NULL
    if (inference_model$beauti_options$beast2_version != "2.6") {
        trait_set_str <- create_trait_set_string(utils::read.table(inference_model$tipdates_filename, 
            sep = "\t"))
    }
    first_line <- paste0("<trait id=\"dateTrait.t:", id, "\" ", 
        "spec=\"beast.evolution.tree.TraitSet\" ")
    if (inference_model$beauti_options$beast2_version != "2.6") {
        first_line <- paste0(first_line, "traitname=\"date-forward\" ")
    }
    else {
        first_line <- paste0(first_line, "traitname=\"date\" ")
    }
    first_line <- paste0(first_line, "value=\"", trait_set_str, 
        "\">")
    c(first_line, paste0("    <taxa id=\"TaxonSet.", id, "\" spec=\"TaxonSet\">"), 
        paste0("        <alignment idref=\"", id, "\"/>"), "    </taxa>", 
        "</trait>")
}

Only when the version of beast is not 2.6, inference_model$tipdates_filename would be read. However beastierinstall::install_beast2() automatically installs v2.6. I would like to try v2.7 later.