Hi,
I am trying to run the phylogenize plug-in but I am having problems with it. I think that there is an error with reading the burst12 binary but I have no idea how to solve it. I have checked the permissions and they seem to be alright.
This is the output
sh: /Users/pablo/Downloads/BURST-master/embalmlets/bin/burst12: cannot execute binary file
Quitting from lines 40-110 (phylogenize-report.Rmd)
Error in pz.error(paste0("BURST failed with error code ", r)) :
BURST failed with error code 126
Calls: ⌠read.abd.metadata -> process.16s -> run.burst -> pz.error
In addition: Warning messages:
1: In dir.create(pz.options(âout_dirâ)) :
â/private/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8â already exists
2: In dir.create(pz.options(âout_dirâ)) :
â/private/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8â already exists
3: In dir.create(pz.options(âout_dirâ)) :
â/private/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8â already exists
4: In strsplit(conditionMessage(e), â\nâ) :
input string 1 is invalid in this locale
5: In pz.warning(paste0("sample column not found: ", opts(âsample_columnâ), :
sample column not found: SampleID; assuming row names are sample IDs
Execution halted
Traceback (most recent call last):
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.pyâ, line 150, in _run
Rcmd], check=True)
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/subprocess.pyâ, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command â[âRâ, â-eâ, âsapply(c(âphylogenizeâ, âgraphicsâ, âstatsâ, âmethodsâ,âgrDevicesâ, âbiomformatâ), function(.) library(character.only=TRUE, .));phylogenize::set_data_internal(); phylogenize::render.report(output_file=âindex.htmlâ, report_input=âphylogenize-report.Rmdâ, input_format=âbiomâ, biom_file=âinput.biomâ, burst_dir="/Users/pablo/Downloads/BURST-master/embalmlets/bin/", in_dir="/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8", out_dir="/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8", ncl=1, type=â16Sâ, which_phenotype=âprevalenceâ, which_envir=âInfestedâ, dset_column=âdatasetâ, env_column=âDiagnosticâ, sample_column=âSampleIDâ, burst_cutoff=0.985, assume_below_LOD=TRUE, single_dset=TRUE, minimum=3, treemin=5, relative_out_dir=".", working_dir="/var/folders/3q/m5mw83016g1b5spvgr6444yr0000gn/T/qiime2-temp-2am8ess8")â]â returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.pyâ, line 328, in call
results = action(**arguments)
File â</Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-500>â, line 2, in run
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.pyâ, line 245, in bound_callable
output_types, provenance)
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.pyâ, line 452, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.pyâ, line 41, in run
report_file=âphylogenize-report.Rmdâ)
File â/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.pyâ, line 152, in _run
raise Exception(âError %d in R code!â % e.returncode)
Exception: Error 1 in R code!
Plugin error from phylogenize:
Error 1 in R code!
See above for debug info.
cheers,
Pablo