Comments (12)
Thanks @rscherrer, will work on this today 👍
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Same bug, submitted by Jana Riederer:
please find attached the R code that has been giving me problems.
The error message is:
Error in check_input_filename_validity(input_filename = input_filename, :
'input_filename' must be a valid BEAST2 XML file. File 'C:\Users\User\AppData\Local\Temp\RtmpGqgxlm\beast2_7502ae83371.xml' is not a valid BEAST2 file. FALSE
Attached code:
rm(list=ls())
library(babette)
#load the data
long_data <- "C:\\Users\\User\\Documents\\Groningen\\BEE\\phylogen\\primates_long.fas"
testit::assert(file.exists(long_data))
mcmc <- create_mcmc(chain_length = 100000, store_every = 1000)
#choose site model
site_model <- create_gtr_site_model()
#choose clock model
clock_model <- create_rln_clock_model()
#create a tree prior
tree_prior <- create_tree_prior_bd
#calibrating the tree using mrca
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = long_data),
taxa_names = get_taxa_names(filename = long_data)[1:2],
is_monophyletic = TRUE
)
mrca_distr <- create_normal_distr(
mean = 15.0,
sigma = 1.0
)
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = long_data),
taxa_names = get_taxa_names(filename = long_data),
mrca_distr = mrca_distr
)
#posterior crown age
out <- bbt_run(
fasta_filenames = long_data,
mrca_priors = create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = long_data),
taxa_names = get_taxa_names(filename = long_data),
mrca_distr = create_normal_distr(
mean = 15.0,
sigma = 0.0001
)
),
mcmc = mcmc,
site_models = site_model,
clock_models = clock_model,
tree_priors = tree_prior()
)
#plot it
plot_densitree(out$primates_long_trees [80:101], width = 2)
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Will try to fix again on Friday Nov 9th.
from babette.
babetter reproduces all these bugs
from babette.
Easiest will be JC69 relaxed_log_normal yule
, exactly the combination of @rscherrer
from babette.
Mysterious, I test for this already in anthus_aco_sub_calibrated_rln_monophyletic.xml
, which passes already...
(and yes, the file anthus_aco_sub_calibrated_rln_monophyletic.xml
is valid)
from babette.
Note that Raphael uses a non-monophyletic and Jana use a monophyletic MRCA prior...
from babette.
Without an MRCA distribution, this works fine.
from babette.
I tried to redo the non-monophyletic setting (it is closest to default), and spot already some clear differences:
from babette.
The error message is this:
File: created.xml seed: 1541749704191 threads: 1
Error 170 parsing the xml input file
Could not find object associated with idref clockRate.c:anthus_aco_sub
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<operator id='StrictClockRateScaler.c:anthus_aco_sub' spec='ScaleOperator'>
<input>
java.lang.UNIXProcess$ProcessPipeInputStream@9807454
from babette.
babetter confirms this Issue is resolved. Thanks @rscherrer and Jana Riederer.
from babette.
Problem is in the header, the first line :-/ ?
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