Hi Everyone!
I'm also having some issues with this plugin. I was able to install the plugin with no problems. However, when I try to run:
looking for file: /tmp/qiime2-temp-8rktczvl/input.biom
located biom file: /tmp/qiime2-temp-8rktczvl/input.biom
Calling BURST with arguments: -r /home/fstudart/anaconda3/envs/qiime2-2019.10/lib/R/library/phylogenize/extdata/16s_renamed.frn -fr -q /tmp/qiime2-temp-8rktczvl/input_seqs.txt -i 0.985 -o /tmp/qiime2-temp-8rktczvl/output_assignments.txt
sh: 1: /usr/local/bin/burst12: not found
Quitting from lines 40-110 (phylogenize-report.Rmd)
Error in pz.error(paste0("BURST failed with error code ", r)) :
BURST failed with error code 127
Calls: ... read.abd.metadata -> process.16s -> run.burst -> pz.error
In addition: Warning messages:
1: In dir.create(pz.options("out_dir")) :
'/tmp/qiime2-temp-8rktczvl' already exists
2: In dir.create(pz.options("out_dir")) :
'/tmp/qiime2-temp-8rktczvl' already exists
3: In dir.create(pz.options("out_dir")) :
'/tmp/qiime2-temp-8rktczvl' already exists
4: In strsplit(conditionMessage(e), "\n") :
input string 1 is invalid in this locale
5: In pz.warning(paste0("sample column not found: ", opts("sample_column"), :
sample column not found: SampleID; assuming row names are sample IDs
6: In system2(file.path(opts("burst_dir"), opts("burst_bin")), args = burst_args) :
error in running command
Execution halted
Traceback (most recent call last):
File "/home/fstudart/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.py", line 150, in _run
Rcmd], check=True)
File "/home/fstudart/anaconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['R', '-e', 'sapply(c("phylogenize", "graphics", "stats", "methods","grDevices", "biomformat"), function(.) library(character.only=TRUE, .));phylogenize::set_data_internal(); phylogenize::render.report(output_file="index.html", report_input="phylogenize-report.Rmd", input_format="biom", biom_file="input.biom", burst_dir="/usr/local/bin", in_dir="/tmp/qiime2-temp-8rktczvl", out_dir="/tmp/qiime2-temp-8rktczvl", ncl=1, type="16S", which_phenotype="prevalence", which_envir="Saliva", dset_column="dataset", env_column="Quality", sample_column="SampleID", burst_cutoff=0.985, assume_below_LOD=TRUE, single_dset=TRUE, minimum=3, treemin=5, relative_out_dir=".", working_dir="/tmp/qiime2-temp-8rktczvl")']' returned non-zero exit status 1.
In my case, I'm using Linux 19.10 through VirtualBox (host OS: Windows 10).
I'm also including the output of library(phylogenize):
library(phylogenize)
Loading required package: phylolm
Loading required package: ape
Loading required package: settings
Loading required package: Matrix
Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
ggplot2 3.2.1 purrr 0.3.3
tibble 2.1.3 dplyr 0.8.3
tidyr 1.0.0 stringr 1.4.0
readr 1.3.1 forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
tidyr::expand() masks Matrix::expand()
dplyr::filter() masks stats::filter()
dplyr::lag() masks stats::lag()
tidyr::pack() masks Matrix::pack()
tidyr::unpack() masks Matrix::unpack()
Loading required package: ggtree
ggtree v1.14.6 For help: ggtree
If you use ggtree in published research, please cite the most appropriate paper(s):
-
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
-
Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194
Attaching package: ‘ggtree’
The following object is masked from ‘package:tidyr’:
expand
The following object is masked from ‘package:Matrix’:
expand
The following object is masked from ‘package:ape’:
rotate
Loading required package: biomformat
Loading required package: functional
Loading required package: future
Loading required package: furrr
I'm not an expert, but how it seems that I'm missing the burst dependencies, right? Ho can I download them?
Thanks in advance,
FS