Describe the bug I apologize for disturbing you, I've recently tr

Ah, it is not on CRAN yet. Try: <div class="highlight highlight-source-r notransla

And I predict I will ask you to do after that 😁👍 <div class="highlight highlight

Reproduced error, with verbose settings: <div class="snippet-clipboard-content not

Problem with "tipdates_filename",about ropensci/babette

Comments (38)

geofrunz commented on August 19, 2024 1

Here the report! thank you so much!

beastier::beastier_report()

beastier *

OS: unix

Dependencies *

beautier version: 2.3.6
beastier version: 2.1.3

BEAST2 *

Java version: 11.0.7+10-post-Ubuntu-2ubuntu218.04
Is BEAST2 installed: TRUE
BEAST2 version: 2.6.1
BEAST2 default path: /home/giovanni/.local/share/beast/bin/beast

sessionInfo *

R version 3.6.3 (2020-02-29)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS/LAPACK: /home/giovanni/anaconda3/envs/CoronaEv/lib/libopenblasp-r0.3.7.so

locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 LC_PAPER=it_IT.UTF-8 LC_NAME=it_IT.UTF-8
[9] LC_ADDRESS=it_IT.UTF-8 LC_TELEPHONE=it_IT.UTF-8 LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=it_IT.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rJava_0.9-12 babette_2.1.2 tracerer_2.1 mauricer_2.0.6 beastier_2.1.3 beautier_2.3.6

loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 knitr_1.29 magrittr_1.5 MASS_7.3-51.6
[5] rappdirs_0.3.1 assertive.data.us_0.0-2 testit_0.11 lattice_0.20-41
[9] ape_5.4 assertive.code_0.0-3 assertive.reflection_0.0-4 stringr_1.4.0
[13] assertive.matrices_0.0-2 tools_3.6.3 assertive.properties_0.0-4 parallel_3.6.3
[17] grid_3.6.3 nlme_3.1-148 xfun_0.15 seqinr_3.6-1
[21] assertive.models_0.0-2 assertive.files_0.0-2 ade4_1.7-15 yaml_2.2.1
[25] assertive.base_0.0-7 assertive.data_0.0-3 pryr_0.1.4 assertive.sets_0.0-3
[29] assertive.datetimes_0.0-2 assertive.types_0.0-3 codetools_0.2-16 stringi_1.4.6
[33] compiler_3.6.3 assertive.data.uk_0.0-2 assertive.numbers_0.0-2 assertive.strings_0.0-3
[37] assertive_0.3-5

from babette.

geofrunz commented on August 19, 2024 1

Thank you so much!!!
you are really kind!
No hurry at all!!
let me know if I can be of any help
Very best regards
Giovanni

from babette.

richelbilderbeek commented on August 19, 2024

Hi Giovanni,

Thanks for you -AFAICS awesome!- bugreport.

What is missing is the result of beastier::beastier_report(). Could you paste it as well? After that, I will happily take a look 👍

from babette.

geofrunz commented on August 19, 2024

Thank you for your immediate reply...
actually, when I tried to run
beastier::beastier_report() after the script, I get:
"'beastier_report' non è un oggetto esportato dal 'namespace:beastier'"
translated: "beastier_report" is not an object exported from "namespace:beastier"..
However, I had no troubles in loading the library(beastier)
When/where should I run it? sorry again...

from babette.

richelbilderbeek commented on August 19, 2024

No worries!

Sounds like you got an old package.

Try updating the package beastier, so you can actually run that report 👍

Actually, that alone may already fix your problem 😎 👍

from babette.

geofrunz commented on August 19, 2024

I'm running beastier version 2.1.1
I tried update_babette() and update_beastier() but nothing changed...
I get the same message..

from babette.

richelbilderbeek commented on August 19, 2024

Ah, it is not on CRAN yet. Try:

remotes::install_github("ropensci/beastier")

Then I'd enjoy to see the report 👍

from babette.

richelbilderbeek commented on August 19, 2024

And I predict I will ask you to do after that 😁👍

remotes::install_github("ropensci/beautier")
beastier::uninstall_beast2()
beastier::install_beast2()

from babette.

richelbilderbeek commented on August 19, 2024

Reproduced error, with verbose settings:

>   out <- bbt_run_from_model(
+     fasta_filename = filename,
+     beast2_options = create_beast2_options(verbose = TRUE) ,
+     inference_model = inference_model
+   )
|                      |value                                              |
|:---------------------|:--------------------------------------------------|
|input_filename        |/home/richel/.cache/beast2_12cda71fddec.xml        |
|output_state_filename |/home/richel/.cache/beast2_12cda1c66cdf0.xml.state |
|rng_seed              |NA                                                 |
|n_threads             |NA                                                 |
|use_beagle            |FALSE                                              |
|overwrite             |TRUE                                               |
|beast2_path           |/home/richel/.local/share/beast/lib/launcher.jar   |
|verbose               |TRUE                                               |
|                           |value                                              |
|:--------------------------|:--------------------------------------------------|
|input_filename_full        |/home/richel/.cache/beast2_12cda71fddec.xml        |
|output_state_filename_full |/home/richel/.cache/beast2_12cda1c66cdf0.xml.state |
 [1] ""                                                                                                   
 [2] "                        BEAST v2.6.2, 2002-2020"                                                    
 [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] "                       [email protected]"                                                  
[10] "                        [email protected]"                                                   
[11] "                                    "                                                               
[12] "                   Institute of Evolutionary Biology"                                               
[13] "                        University of Edinburgh"                                                    
[14] "                           [email protected]"                                                      
[15] "                                    "                                                               
[16] "                    David Geffen School of Medicine"                                                
[17] "                 University of California, Los Angeles"                                             
[18] "                           [email protected]"                                                       
[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: 1593172414367"                                                                  
[36] ""                                                                                                   
[37] "File: beast2_12cda71fddec.xml seed: 1593172414367 threads: 1"                                       
[38] "Loading package NS v1.1.0"                                                                          
[39] "Loading package BEAST v2.6.2"                                                                       
[40] "Loading package BEASTLabs v1.9.4"                                                                   
[41] "Loading package MODEL_SELECTION v1.5.3"                                                             
[42] "Loading package BEAST v2.6.2"                                                                       
[43] ""                                                                                                   
[44] "Error 170 parsing the xml input file"                                                               
[45] ""                                                                                                   
[46] "Could not find object associated with idref clockRate.c:Felinecoronavirus_Envelope_1"               
[47] ""                                                                                                   
[48] "Error detected about here:"                                                                         
[49] "  <beast>"                                                                                          
[50] "      <run id='mcmc' spec='MCMC'>"                                                                  
[51] "          <operator id='StrictClockRateScaler.c:Felinecoronavirus_Envelope_1' spec='ScaleOperator'>"
[52] "              <input>"                                                                              
[53] ""                                                                                                   
attr(,"status")
[1] 1
 [1] ""                                                                                                   
 [2] "                        BEAST v2.6.2, 2002-2020"                                                    
 [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] "                       [email protected]"                                                  
[10] "                        [email protected]"                                                   
[11] "                                    "                                                               
[12] "                   Institute of Evolutionary Biology"                                               
[13] "                        University of Edinburgh"                                                    
[14] "                           [email protected]"                                                      
[15] "                                    "                                                               
[16] "                    David Geffen School of Medicine"                                                
[17] "                 University of California, Los Angeles"                                             
[18] "                           [email protected]"                                                       
[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: 1593172415044"                                                                  
[36] ""                                                                                                   
[37] "File: beast2_12cda71fddec.xml seed: 1593172415044 threads: 1"                                       
[38] "Loading package NS v1.1.0"                                                                          
[39] "Loading package BEAST v2.6.2"                                                                       
[40] "Loading package BEASTLabs v1.9.4"                                                                   
[41] "Loading package MODEL_SELECTION v1.5.3"                                                             
[42] "Loading package BEAST v2.6.2"                                                                       
[43] ""                                                                                                   
[44] "Error 170 parsing the xml input file"                                                               
[45] ""                                                                                                   
[46] "Could not find object associated with idref clockRate.c:Felinecoronavirus_Envelope_1"               
[47] ""                                                                                                   
[48] "Error detected about here:"                                                                         
[49] "  <beast>"                                                                                          
[50] "      <run id='mcmc' spec='MCMC'>"                                                                  
[51] "          <operator id='StrictClockRateScaler.c:Felinecoronavirus_Envelope_1' spec='ScaleOperator'>"
[52] "              <input>"                                                                              
[53] ""                                                                                                   
attr(,"status")
[1] 1

from babette.

richelbilderbeek commented on August 19, 2024

Hmmm, the txt and csv files look solid to me 🤔

from babette.

richelbilderbeek commented on August 19, 2024

The created XML:

<?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="Felinecoronavirus_Envelope_1"
name="alignment">
                    <sequence id="seq_FJ938051.1|Felinecoronavirus|cat|USACalifornia|2002|Envelope" taxon="FJ938051.1|Felinecoronavirus|cat|USACalifornia|2002|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgcaatttaggtaagactattatagtactacctgcacgccatgcatatgatgcctataagaactttatgcagatyaaggcatataatcccgacgaagcacttttggtttga"/>
                    <sequence id="seq_FJ938053.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938053.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgtcagcgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatttgggtaagactattatagtattacctgcacgccatgcatatgatgcctacaagacctttatgcaaattaaggcatataatcccgacgaagcattcttggtttga"/>
                    <sequence id="seq_FJ938054.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938054.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgtcagcgtcttctttttgctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatttgggtaagactattatagtattacctgcacgccatgcatatgatgcctacaagacctttatgcaaattaaggcatataaccccgacgaagcattcttggtttga"/>
                    <sequence id="seq_FJ938055.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938055.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggtcgttagcgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatctgggtaagactattatagtactacctgctcgccatgcgtatgatgcctataagacttttatgcagattaaggcatacaatcccgacgaagcatttttggtttga"/>
                    <sequence id="seq_FJ938057.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938057.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttyctagggcatttactatcatagatgaccacggcatggtcgttagtgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgcaatttaggtaagactattatagtactaccggcgcgccatgcatatgatgcctacaasaattttatgcaaataaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_FJ938058.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938058.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagcgtcttcttttggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtgtgttgcaatttgggtaagactattatagtactacctgcacgccatgcatatgatgcctacaagacctttatgcaaattaaggcatataatcccgacgaagcatttctggtttga"/>
                    <sequence id="seq_FJ938060.1|Felinecoronavirus|cat|USACalifornia|1993|Envelope" taxon="FJ938060.1|Felinecoronavirus|cat|USACalifornia|1993|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_FJ938061.1|Felinecoronavirus|cat|USACalifornia|1998|Envelope" taxon="FJ938061.1|Felinecoronavirus|cat|USACalifornia|1998|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_FJ938062.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" taxon="FJ938062.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgtcagcgtcttcttctggctcctgttgataattatattgatattgttctcaatagcattgctaaatgttattaaattgtgcatggtatgttgcaatttgggtaagactattatagtactaccagcacgccatgtctatgatgcctataagacttttatgcagatcaaggcatataatcccgacgaagcattcttggtttga"/>
                    <sequence id="seq_GU553362.1|Felinecoronavirus|feline|Netherlands|2007|Envelope" taxon="GU553362.1|Felinecoronavirus|feline|Netherlands|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttaccatcatagatgaccatggcatggttgtcagtgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtttgttgcaatttgggtaagactattatagtactacctgcacgccatgcatatgatgcctataagacttttatgcagattaaggcatataaccccgatgaagcatttttggtttga"/>
                    <sequence id="seq_HQ012367.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" taxon="HQ012367.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttccttgggcatttactatcatagatgaccatggtatggtagttagtgtcttcttttggctcctgttgataatcatattgatattgttttcaatagcattgctaaatgttattaaagtgtgcatggtgtgctgcaatttgggtaagactatcatagtactacccgcacgccatgcatatgatgcctataagacctttatgcagattaaggcatataatcccgacgaagcatttttggtttga"/>
                    <sequence id="seq_HQ012368.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" taxon="HQ012368.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggcatggtcgttagtgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgctgcaatttaggtaagactattatagtactaccggcacgccatgcatatgatgcctacaagaattttatgcaaataaaggcatataatcccgacgaagcatttttagtttga"/>
                    <sequence id="seq_HQ012370.1|Felinecoronavirus|feline|Netherlands|2008|Envelope" taxon="HQ012370.1|Felinecoronavirus|feline|Netherlands|2008|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagcgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatttgggtaagactattatagtactacctgtacgccatgcatatgatgcctataagacctttatgcagattaaggcatataattctgacgaagcactcttggtttga"/>
                    <sequence id="seq_HQ392469.1|Felinecoronavirus|Feliscatus|Netherlands|2008|Envelope" taxon="HQ392469.1|Felinecoronavirus|Feliscatus|Netherlands|2008|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgtaagcgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattatgtatggtttgttgcgatttaggtaaaactattatagtactacctgcacgccatgcgtatgatgcctataagacctttatgcagattaaggcatataatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_HQ392470.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" taxon="HQ392470.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtgtgctgcaatttgggtaagactatcatagtactacccgcacgccatgcatatgatgcctataagacctttatgcagattaaggcatataatcccgacgaagcatttttggtttga"/>
                    <sequence id="seq_KC461236.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope" taxon="KC461236.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope" totalcount="4" value="atgacgttccctagggcatttactatcatagatgaccatggcatggttgttagcgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgcaatttgggtaagactattatagtactacctgcacgccatgcatatgatgcctataagacctttatgcaaaccaaggcatataatcccgacgaagcatttttggtttga"/>
                    <sequence id="seq_KC461237.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope" taxon="KC461237.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope" totalcount="4" value="atgacgttccctagggcatttactatcatagatgaccatggcatggttgttagcgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgcaatttgggtaagactattatagtactacctgcacgccatgcatatgatgcctataagacctttatgcaaaccaaggcatataatcccgacgaagcatttttggtttga"/>
                    <sequence id="seq_KP143507.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" taxon="KP143507.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgttagtgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgtaatttgggtaagactattatagtattacccgctcgccatgcatatgatgcctataagacctttatgcaaattaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_KP143509.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" taxon="KP143509.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgttagtgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgtaatttgggtaagactattatagtattacccgctcgccatgcatatgatgcctataagacctttatgcaaattaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_KP143510.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" taxon="KP143510.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgttagtgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgtaatttgggtaagactattatagtattacccgctcgccatgcatatgatgcctataagacctttatgcaaattaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_KP143511.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" taxon="KP143511.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgttagtgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgtaatttgggtaagactattatagtattacccgctcgccatgcatatgatgcctataagacctttatgcaaattaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_KP143512.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" taxon="KP143512.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgttagtgtcttcttctggctcctgttgataattgtattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtatgttgtaatttgggtaagactattatagtattacccgctcgccatgcatatgatgcctataagacctttatgcaaattaaggcatataatcccgacgaagcattcttagtttga"/>
                    <sequence id="seq_KU215420.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" taxon="KU215420.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_KU215423.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" taxon="KU215423.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_KU215424.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" taxon="KU215424.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_KU215427.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" taxon="KU215427.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgttagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttatcaaattgtgcatggtgtgttgcaatttaggtaagactattatagtactacctgcacgccatgcgtatgatgcctataagaactttatgcatattaaggcatatgatcccgatgaagcattcttggtttga"/>
                    <sequence id="seq_KX722530.1|Felinecoronavirus|Feliscatus|Denmark|2015|Envelope" taxon="KX722530.1|Felinecoronavirus|Feliscatus|Denmark|2015|Envelope" totalcount="4" value="atgatgtttcctagggcttttactatcatagatgaccatggtatggttgtaagcgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtttgttgcaatctgggtaagactattatagtactacctgcacgccatgcatatgatgcctacaagacttttatgcaaattaaggcatataatcccgacgaagcacttttggtttga"/>
                    <sequence id="seq_KY292377.1|Felinecoronavirus|cat|China|2016|Envelope" taxon="KY292377.1|Felinecoronavirus|cat|China|2016|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagacgaccatggtatggttgtcagcgtattcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatttgggtaagactatcatagtactacctgctcgccatgcatatgatgcctataagacatttatgcaaattaaggcatataatcctgatgaagcattcttggtttga"/>
                    <sequence id="seq_KY566211.1|Felinecoronavirus|cat|China|2016|Envelope" taxon="KY566211.1|Felinecoronavirus|cat|China|2016|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggcatggttattagtgtcttcttctggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaaattgtgcatggtgtgttgcaatttgggtaagactatcatagtactacctgcacgccatgcatatgatgcctataagacatttatgcgaattaaggcatataatcctgacgaagcattcttggtttga"/>
                    <sequence id="seq_MG893511.1|Felinecoronavirus|Feliscatus|Germany|2012|Envelope" taxon="MG893511.1|Felinecoronavirus|Feliscatus|Germany|2012|Envelope" totalcount="4" value="atgatgtttcctagggcatttactatcatagatgaccatggtatggttgtgagcgtcttcttttggctcctgttgataattatattgatattgttttcaatagcattgctaaatgttattaagttatgcatggtatgttgcaatttgggtaatactattatagtgttacctgcacgccacgcatatgatgcctataagacttttatgcagattaaggcatataatcccgatgaagcattctcggtttga"/>
                </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="10000">
    <state id="state" storeEvery="5000">
        <tree id="Tree.t:Felinecoronavirus_Envelope_1" name="stateNode">
            <trait id="dateTrait.t:Felinecoronavirus_Envelope_1" spec="beast.evolution.tree.TraitSet" traitname="date-forward" value="KX722530.1|Felinecoronavirus|Feliscatus|Denmark|2015|Envelope=2015,FJ938053.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,GU553362.1|Felinecoronavirus|feline|Netherlands|2007|Envelope=2007,KP143512.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope=2013,KU215424.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope=2013,HQ392470.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope=2007,KY566211.1|Felinecoronavirus|cat|China|2016|Envelope=2016,KP143510.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope=2013,FJ938057.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,MG893511.1|Felinecoronavirus|Feliscatus|Germany|2012|Envelope=2012,FJ938055.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,FJ938054.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,HQ012368.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope=2007,FJ938058.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,KY292377.1|Felinecoronavirus|cat|China|2016|Envelope=2016,FJ938060.1|Felinecoronavirus|cat|USACalifornia|1993|Envelope=1993,KU215427.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope=2013,KC461236.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope=2011,KP143509.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope=2013,KC461237.1|Felinecoronavirus|Feliscatus|USA|2011|Envelope=2011,HQ392469.1|Felinecoronavirus|Feliscatus|Netherlands|2008|Envelope=2008,KU215423.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope=2013,FJ938062.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope=2007,KP143507.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope=2013,FJ938051.1|Felinecoronavirus|cat|USACalifornia|2002|Envelope=2002,HQ012370.1|Felinecoronavirus|feline|Netherlands|2008|Envelope=2008,HQ012367.1|Felinecoronavirus|feline|NetherlandsUtrecht|2007|Envelope=2007,FJ938061.1|Felinecoronavirus|cat|USACalifornia|1998|Envelope=1998,KU215420.1|Felinecoronavirus|Feliscatus|Belgium|2013|Envelope=2013,KP143511.1|Felinecoronavirus|Feliscatus|UnitedKingdom|2013|Envelope=2013">
                <taxa id="TaxonSet.Felinecoronavirus_Envelope_1" spec="TaxonSet">
                    <alignment idref="Felinecoronavirus_Envelope_1"/>
                </taxa>
            </trait>
            <taxonset idref="TaxonSet.Felinecoronavirus_Envelope_1"/>
        </tree>
        <parameter id="ucldStdev.c:Felinecoronavirus_Envelope_1" lower="0.0" name="stateNode">0.1</parameter>
        <stateNode id="rateCategories.c:Felinecoronavirus_Envelope_1" spec="parameter.IntegerParameter" dimension="58">1</stateNode>
        <parameter id="bPopSizes.t:Felinecoronavirus_Envelope_1" dimension="5" lower="0.0" name="stateNode" upper="380000.0">380.0</parameter>
        <stateNode id="bGroupSizes.t:Felinecoronavirus_Envelope_1" spec="parameter.IntegerParameter" dimension="5">1</stateNode>
    </state>

    <init id="RandomTree.t:Felinecoronavirus_Envelope_1" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:Felinecoronavirus_Envelope_1" taxa="@Felinecoronavirus_Envelope_1">
        <populationModel id="ConstantPopulation0.t:Felinecoronavirus_Envelope_1" spec="ConstantPopulation">
            <parameter id="randomPopSize.t:Felinecoronavirus_Envelope_1" name="popSize">1.0</parameter>
        </populationModel>
    </init>

    <distribution id="posterior" spec="util.CompoundDistribution">
        <distribution id="prior" spec="util.CompoundDistribution">
            <distribution id="BayesianSkyline.t:Felinecoronavirus_Envelope_1" spec="BayesianSkyline" groupSizes="@bGroupSizes.t:Felinecoronavirus_Envelope_1" popSizes="@bPopSizes.t:Felinecoronavirus_Envelope_1">
                <treeIntervals id="BSPTreeIntervals.t:Felinecoronavirus_Envelope_1" spec="TreeIntervals" tree="@Tree.t:Felinecoronavirus_Envelope_1"/>
            </distribution>
            <distribution id="MarkovChainedPopSizes.t:Felinecoronavirus_Envelope_1" spec="beast.math.distributions.MarkovChainDistribution" jeffreys="true" parameter="@bPopSizes.t:Felinecoronavirus_Envelope_1"/>
            <prior id="ucldStdevPrior.c:Felinecoronavirus_Envelope_1" name="distribution" x="@ucldStdev.c:Felinecoronavirus_Envelope_1">
                <Gamma id="Gamma.0" name="distr">
                    <parameter id="RealParameter.0" estimate="false" name="alpha">0.5396</parameter>
                    <parameter id="RealParameter.1" estimate="false" name="beta">0.3819</parameter>
                </Gamma>
            </prior>
        </distribution>
        <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
            <distribution id="treeLikelihood.Felinecoronavirus_Envelope_1" spec="ThreadedTreeLikelihood" data="@Felinecoronavirus_Envelope_1" tree="@Tree.t:Felinecoronavirus_Envelope_1">
                <siteModel id="SiteModel.s:Felinecoronavirus_Envelope_1" spec="SiteModel">
                    <parameter id="mutationRate.s:Felinecoronavirus_Envelope_1" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:Felinecoronavirus_Envelope_1" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:Felinecoronavirus_Envelope_1" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="JC69.s:Felinecoronavirus_Envelope_1" spec="JukesCantor"/>
                </siteModel>
                <branchRateModel id="RelaxedClock.c:Felinecoronavirus_Envelope_1" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" rateCategories="@rateCategories.c:Felinecoronavirus_Envelope_1" tree="@Tree.t:Felinecoronavirus_Envelope_1">
                    <LogNormal id="LogNormalDistributionModel.c:Felinecoronavirus_Envelope_1" S="@ucldStdev.c:Felinecoronavirus_Envelope_1" meanInRealSpace="true" name="distr">
                        <parameter id="RealParameter.4" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
                    </LogNormal>
                    <parameter id="ucldMean.c:Felinecoronavirus_Envelope_1" estimate="false" name="clock.rate">0.001</parameter>
                </branchRateModel>
            </distribution>
        </distribution>
    </distribution>

    <operator id="popSizesScaler.t:Felinecoronavirus_Envelope_1" spec="ScaleOperator" parameter="@bPopSizes.t:Felinecoronavirus_Envelope_1" scaleFactor="0.75" weight="15.0"/>

    <operator id="groupSizesDelta.t:Felinecoronavirus_Envelope_1" spec="DeltaExchangeOperator" integer="true" weight="6.0">
        <intparameter idref="bGroupSizes.t:Felinecoronavirus_Envelope_1"/>
    </operator>

    <operator id="BayesianSkylineTreeScaler.t:Felinecoronavirus_Envelope_1" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="3.0"/>

    <operator id="BayesianSkylineTreeRootScaler.t:Felinecoronavirus_Envelope_1" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="3.0"/>

    <operator id="BayesianSkylineUniformOperator.t:Felinecoronavirus_Envelope_1" spec="Uniform" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="30.0"/>

    <operator id="BayesianSkylineSubtreeSlide.t:Felinecoronavirus_Envelope_1" spec="SubtreeSlide" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="15.0"/>

    <operator id="BayesianSkylineNarrow.t:Felinecoronavirus_Envelope_1" spec="Exchange" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="15.0"/>

    <operator id="BayesianSkylineWide.t:Felinecoronavirus_Envelope_1" spec="Exchange" isNarrow="false" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="3.0"/>

    <operator id="BayesianSkylineWilsonBalding.t:Felinecoronavirus_Envelope_1" spec="WilsonBalding" tree="@Tree.t:Felinecoronavirus_Envelope_1" weight="3.0"/>

    <operator id="ucldStdevScaler.c:Felinecoronavirus_Envelope_1" spec="ScaleOperator" parameter="@ucldStdev.c:Felinecoronavirus_Envelope_1" scaleFactor="0.5" weight="3.0"/>

    <operator id="CategoriesRandomWalk.c:Felinecoronavirus_Envelope_1" spec="IntRandomWalkOperator" parameter="@rateCategories.c:Felinecoronavirus_Envelope_1" weight="10.0" windowSize="1"/>

    <operator id="CategoriesSwapOperator.c:Felinecoronavirus_Envelope_1" spec="SwapOperator" intparameter="@rateCategories.c:Felinecoronavirus_Envelope_1" weight="10.0"/>

    <operator id="CategoriesUniform.c:Felinecoronavirus_Envelope_1" spec="UniformOperator" parameter="@rateCategories.c:Felinecoronavirus_Envelope_1" weight="10.0"/>

    <operator id="StrictClockRateScaler.c:Felinecoronavirus_Envelope_1" spec="ScaleOperator" parameter="@clockRate.c:Felinecoronavirus_Envelope_1" scaleFactor="0.75" weight="3.0"/>

    <operator id="strictClockUpDownOperator.c:Felinecoronavirus_Envelope_1" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
        <up idref="clockRate.c:Felinecoronavirus_Envelope_1"/>
        <down idref="Tree.t:Felinecoronavirus_Envelope_1"/>
    </operator>

    <logger id="tracelog" fileName="Felinecoronavirus_Envelope_1.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
        <log idref="posterior"/>
        <log idref="likelihood"/>
        <log idref="prior"/>
        <log idref="treeLikelihood.Felinecoronavirus_Envelope_1"/>
        <log id="TreeHeight.t:Felinecoronavirus_Envelope_1" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:Felinecoronavirus_Envelope_1"/>
        <log idref="ucldStdev.c:Felinecoronavirus_Envelope_1"/>
        <log id="rate.c:Felinecoronavirus_Envelope_1" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:Felinecoronavirus_Envelope_1" tree="@Tree.t:Felinecoronavirus_Envelope_1"/>
        <log idref="BayesianSkyline.t:Felinecoronavirus_Envelope_1"/>
        <log idref="bPopSizes.t:Felinecoronavirus_Envelope_1"/>
        <log idref="bGroupSizes.t:Felinecoronavirus_Envelope_1"/>
        <log idref="clockRate.c:Felinecoronavirus_Envelope_1"/>
    </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:Felinecoronavirus_Envelope_1" fileName="$(tree).trees" logEvery="1000" mode="tree">
        <log id="TreeWithMetaDataLogger.t:Felinecoronavirus_Envelope_1" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:Felinecoronavirus_Envelope_1" tree="@Tree.t:Felinecoronavirus_Envelope_1"/>
    </logger>

</run>

</beast>

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richelbilderbeek commented on August 19, 2024

Something maybe unrelated, but post it here for myself:

When reading the tipdates file from BEAUti, this fails:

Maybe the numbers must be surrounded by double quotes as well?

"KX722530.1|Felinecoronavirus|Feliscatus|Denmark|2015|Envelope"	2015
"FJ938053.1|Felinecoronavirus|cat|NetherlandsUtrecht|2007|Envelope"	2007
"GU553362.1|Felinecoronavirus|feline|Netherlands|2007|Envelope"	2007

Still, this does not appear to be the main issue for now 👍

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richelbilderbeek commented on August 19, 2024

Also, this does work in BEAUti:

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richelbilderbeek commented on August 19, 2024

I learn from the beautier file G_VII_pre2003_dates_4.txt, that there are no quotes:

KF767106_Indonesia_1976_VII	1976
KF767104_Indonesia_1988_VII	1988
KF767105_Indonesia_1988_VII	1988

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richelbilderbeek commented on August 19, 2024

Nope, removing the quotes has no effect.

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richelbilderbeek commented on August 19, 2024

Loading file without quotes in BEAUti does work as expected:

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richelbilderbeek commented on August 19, 2024

Create a BEAUti file from it, in zip.

issue_90.zip

Now this can become a beautier Issue 😁 👍

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richelbilderbeek commented on August 19, 2024

@geofrunz too bad, this may take some time. I will put in some work in this tomorrow.

Thanks for helping me make babette awesome 👍

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richelbilderbeek commented on August 19, 2024

@geofrunz I care about my work and users 👍. I will ask you to verify when it works 😁

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richelbilderbeek commented on August 19, 2024

Due to health Issues, I will work on this July 4th. @geofrunz, I hope the one week day is OK?

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richelbilderbeek commented on August 19, 2024

Will work on it today, for one hour. I was still ill July 4th. Goal: find the minimal reprex.

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richelbilderbeek commented on August 19, 2024

reprex:

test_that("use", {

  filename <- get_babette_path(
    "Felinecoronavirus_Envelope_1.fas"
  )
  tipdates_filename <- get_babette_path(
    "Felinecoronavirus_Envelope_1_no_quotes.txt"
  )
  inference_model <- create_inference_model(
    tipdates_filename = tipdates_filename,
    clock_model = create_rln_clock_model()
  )
  # Could not find object associated with idref clockRate.c:Felinecoronavirus_Envelope_1          # nolint
  #                                                                                               # nolint
  # Error detected about here:                                                                    # nolint
  #                                                                                               # nolint
  # <beast>                                                                                       # nolint
  #   <run id='mcmc' spec='MCMC'>                                                                 # nolint
  #     <operator id='StrictClockRateScaler.c:Felinecoronavirus_Envelope_1' spec='ScaleOperator'> # nolint
  #       <input>                                                                                 # nolint

  expect_silent(
    bbt_run_from_model(
      fasta_filename = filename,
      beast2_options = create_beast2_options(verbose = TRUE),
      inference_model = inference_model
    )
  )
})

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richelbilderbeek commented on August 19, 2024

The error message drops a decent hint: the XML mentions a StrictClockScaler, when there is a RLN clock requested by the user.

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richelbilderbeek commented on August 19, 2024

Moved Issue to ropensci/beautier#117

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richelbilderbeek commented on August 19, 2024

I worked on this the whole Tuesday, cleaning up beautier in the process. Will continue tomorrow.

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geofrunz commented on August 19, 2024

Thank you so much!! You are too kind!! Il giorno mar 7 lug 2020 alle ore 17:52 Richel Bilderbeek < [email protected]> ha scritto:

…

I worked on this the whole Tuesday, cleaning up beautier in the process. Will continue tomorrow. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#90 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACF43AHRITOXNOEXXWP42XDR2NADPANCNFSM4OJCCKVA> .

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richelbilderbeek commented on August 19, 2024

I worked on this the whole Wednesday, cleaning up beautier in the process. Will continue today.

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richelbilderbeek commented on August 19, 2024

Worked on this Thursday and Friday. Will continue on Monday July 20th (I need to do some of my own work as well). I hope that is OK @geofrunz 😅 .

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geofrunz commented on August 19, 2024

More than ok!! Thank you so much! but do not loose to much time on my problems!!! do not worry!! Il giorno lun 13 lug 2020 alle ore 20:52 Richel Bilderbeek < [email protected]> ha scritto:

…

Worked on this Thursday and Friday. Will continue on Monday July 20th (I need to do some of my own work as well). I hope that is OK @geofrunz <https://github.com/geofrunz> 😅 . — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#90 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACF43ADWF7WMFQOJ3OURR7TR3NJWZANCNFSM4OJCCKVA> .

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richelbilderbeek commented on August 19, 2024

Hi @geofrunz, could you still use a bugfix of this? I would guess you have already found a different solution to your problem. If not, I'll continue working on this.

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AlcaArctica commented on August 19, 2024

I encountered a similar issue. However, I just started using babette, so I might have gotten something wrong.
I am running:

out <- if (is_beast2_installed()) {
  inference_model <- create_test_inference_model()
  beast2_options <- create_beast2_options()
  bbt_run(
    fasta_filename = "core.aln",
    tipdates_filename =  "tipdate.tsv",
    site_model = create_jc69_site_model(),
    clock_model = create_rln_clock_model(),                 
    tree_prior = create_yule_tree_prior(),
    mrca_prior = NA,
    mcmc = beautier::create_mcmc(chain_length = 5000),           # adjust chain lenght for shorter run time
    rng_seed = 1,
    overwrite = TRUE,
    verbose = TRUE)
  }

This throws the error message:

[41] "Error 170 parsing the xml input file"                                       
[42] ""                                                                           
[43] "Could not find object associated with idref clockRate.c:core"               
[44] ""                                                                           
[45] "Error detected about here:"                                                 
[46] "  <beast>"                                                                  
[47] "      <run id='mcmc' spec='MCMC'>"                                          
[48] "          <operator id='StrictClockRateScaler.c:core' spec='ScaleOperator'>"
[49] "              <input>"                                                      
[50] ""                                                                           
attr(,"status")
[1] 1
 Show Traceback
 
 Rerun with Debug
 Error in check_input_filename_validity(input_filename = bifs$input_filename_full,  : 
  'input_filename' must be a valid BEAST2 XML file. File '/home/.cache/beast2_1d8ab2f5e4327.xml' is not a valid BEAST2 file. FALSE

The example runs fine when I substitute create_rln_clock_model() for create_strict_clock_model()
Any hints?
Thank you very much

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richelbilderbeek commented on August 19, 2024

This is an awesome bug report (attaching core.aln and tipdate.tsv would make it even more awesome)!

Yup, the RLN clock model is tested (and thus correct) only partially. Getting ropensci/beautier#117 fixed may en passant solve this problem as well. As I have other packages to submit to CRAN first, this is a low priority issue for me (I hoped I would need to fix this for my current postdoc, yet this has not been needed up till now).

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richelbilderbeek commented on August 19, 2024

Another bug report, from our pro user Jason Griffiths:

I figured out the issue and produced a reproducible example for you using the anthus_aco.fas dataset and made up tip dates.

The model with serially observed tips (observations at different times) will work for the strict clock, but not relaxed clock model.

As before the error is:

Error in beastier::check_input_filename_validity(beast2_options) :
  'input_filename' must be a valid BEAST2 XML file. File '/Users/jason/Library/Caches/beast2_4c39463612ed.xml' is not a valid BEAST2 file. FALSE

See line 29 of the code :

inference_model <- create_test_inference_model(
  #clock_model = create_strict_clock_model(), #
  clock_model = create_rln_clock_model(), #
  tree_prior= create_cbs_tree_prior(),
  tipdates_filename=tipdatesfileloc  )

If you comment out the create_rln_clock_model and uncomment create_strict_clock_model, the model will run fine.

I am not sure why this is a problem. I have seen that in beast documentation they can use a relaxed clock model with serial data.

I looked here:
https://taming-the-beast.org/tutorials/FBD-tutorial/FBD-tutorial.pdf
https://taming-the-beast.org/tutorials/Prior-selection/
https://www.beast2.org/files/2015/05/bdskytutorialv2.1.1.pdf

This leads me to think that there is a small bug. What do you think?
Jason

Jason is right (and also found this Issue), this is a known bug.

Will fix it today :-)

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richelbilderbeek commented on August 19, 2024

OK, thes are all the code snippets, with some comments:

These may already work, which is RLN with tipdates:

inference_model <- create_inference_model(
  tipdates_filename = tipdates_filename,
  clock_model = create_rln_clock_model()
)

bbt_run(
  fasta_filename = "core.aln",
  tipdates_filename =  "tipdate.tsv",
  site_model = create_jc69_site_model(),
  clock_model = create_rln_clock_model(),                 
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA
)

Verify RLN with tipdates works, see #99

These are the other examples:

create_inference_model(
  mcmc = create_mcmc(chain_length = 10000),
  tipdates_filename = paste("/home/giovanni/Dropbox/Babette/",gsub(".fas",".txt",f),sep = ""),
  site_model = create_jc69_site_model(),
  clock_model = create_rln_clock_model(mean_clock_rate =  0.001,mean_rate_prior_distr = create_normal_distr()),
  tree_prior = create_cbs_tree_prior()
)

inference_model <- create_test_inference_model(
  #clock_model = create_strict_clock_model(), #
  clock_model = create_rln_clock_model(), #
  tree_prior= create_cbs_tree_prior(),
  tipdates_filename=tipdatesfileloc  
)

Verify RLN + CBS + tipdates

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richelbilderbeek commented on August 19, 2024

Hi @geofrunz and @AlcaArctica, I assume you have lost interest in babette, as it took some time to find a communicative volunteer to try out new versions.

Still, if you want to try out again:

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

Then create an inference model for BEAST 2.6 like this:

create_inference_model(
  # ...
  beauti_options = create_beauti_options_v2_6()
)

I will close this Issue in July 2021.

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geofrunz commented on August 19, 2024

Dear Richel, My apologies, I had troubles with other projects and I had to stop for a while! But I'll try this new version as soon as possible and let you know! thank you so much for your efforts and kindness Geo Il giorno mar 15 giu 2021 alle ore 08:54 Richel Bilderbeek < ***@***.***> ha scritto:

…

Hi @geofrunz <https://github.com/geofrunz> and @AlcaArctica <https://github.com/AlcaArctica>, I assume you have lost interest in babette, as it took some time to find a communicative volunteer to try out new versions. Still, if you want to try out again: remotes::install_github("ropensci/beautier", ref = "develop") Then create an inference model for BEAST 2.6 like this: create_inference_model( # ... beauti_options = create_beauti_options_v2_6() ) I will close this Issue in July 2021. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#90 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACF43AEAPSEF55W3CW4EQ3LTS32KNANCNFSM4OJCCKVA> .

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richelbilderbeek commented on August 19, 2024

Hi @geofrunz, unexpectly fun to hear this just-as-fun reaction! Usually, users try a different tool (and I do the same as well :-) ). No need for apologies, we all have our priorities 😎

Looking forward to a confirmation that it works, or a fresh bug report otherwise. Thanks!

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richelbilderbeek commented on August 19, 2024

Well, this is on CRAN one of these days, so I will assume other users will confirm :-)

Closing this Issue 👍

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Problem with "tipdates_filename" about babette HOT 38 CLOSED

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