Cannot create treelog file 'NA'

[richelbilderbeek]

Describe the bug

I received this question/bug report by email:

I do successfully install beastier and test the function run_beast2 with the example file '2_4.xml'. But when I switch to my own file which is created by windows version of BEAUti2 and run it with run_beast2, the error message pop out: "Error in value[3L] : Cannot create treelog file 'NA'". I compared the structure of the example files and my file and cannot figure out where is the problem.

I check the version of BEAST2 install by beastier and my windows version of BEAST2. They are the same v2.6.0. So this should not be the problem.

The BEAUti file is attached:
Step_4_1_BEAUti_output.zip

To Reproduce

I guess running the XML with beastier, something like:

beastier::run_beast2_from_file("Step_4_1_BEAUti_output.xml")

Expected behavior

Does a BEAST2 run from the script

Screenshots

If applicable, add screenshots to help explain your problem.

Environment:
Show the results of running the following script:

library(beastier)
beastier::beastier_report()

Additional context
Add any other context about the problem here.

[richelbilderbeek]

I predict that something like create_beast2_options_v2_6() must be run.

[richelbilderbeek]

By email:

[...] I tried to creat the beast2 input file through the function 'create_beast2_input_file'. My code is:

> create_beast2_input_file(
  'Step 2.3 COI haplotype matrix.fasta',
  site_model = create_gtr_site_model(gamma_site_model = create_gamma_site_model()),
  output_filename = 'Step 4.1 BEAUti output by babette.xml',
  mcmc = create_mcmc(
    chain_length = 9e+07,
    store_every = -1,
    pre_burnin = 0,
    n_init_attempts = 10,
    sample_from_prior = FALSE,
    tracelog = create_tracelog(filename = "Step 4.2 COI BEAST output.log", log_every = 9000),
    screenlog = create_screenlog(log_every = 9000),
    treelog = create_treelog(filename = "Step 4.2 COI BEAST output.trees",log_every = 9000)),
    beauti_options = create_beauti_options_v2_6()
  )

BTW, I guess you mean beauti_options = create_beauti_options_v2_6() rather than beast2_options. Then I execute:

> run_beast2(input_filename = "Step 4.1 BEAUti output by babette.xml")
> run_beast2(input_filename = "Step 4.1 BEAUti output by BEAST v2.6.0.xml")

which give the same error message: "Error in value[[3L]](cond) : Cannot create treelog file 'NA'".

However, the above two xml are executable in BEAST v2.6.0 (see attached screenshot together with files that I have mentioned). Weird!

[richelbilderbeek]

My next hypothesis is that the filenames are not allowed to contain spaces. Let's see ...

[richelbilderbeek]

It is the spaces that cause the error, as extract_treelog_filename_from_beast2_input_file has regexps that assume no spaces.

check_can_create_treelog_file <- function(
  beast2_options
) {
  # Extract the treelog file
  testthat::expect_true(file.exists(beast2_options$input_filename))
  treelog_filename <- beastier::extract_treelog_filename_from_beast2_input_file(
    input_filename = beast2_options$input_filename
  )

[richelbilderbeek]

beautier no disallows spaces in filenames.