error plugin q2-phylogenize

Hi all,

I am trying to install and run q2-phylogenize on Qiime for first Moving pictures data to further use it for my own data. After install it as proposed in their own page I am getting the follow error after running this script:

Script:
Running phylogenize in R…
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="/root/miniconda3/pkgs/burst-v0.99.8-0/bin/", in_dir="/tmp/qiime2-temp-0cz9j6vy", out_dir="/tmp/qiime2-temp-0cz9j6vy", ncl=1, type=“16S”, which_phenotype=“prevalence”, which_envir=“gut”, dset_column=“dataset”, env_column=“BodySite”, 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-0cz9j6vy")

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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="/root/miniconda3/pkgs/burst-v0.99.8-0/bin/", in_dir="/tmp/qiime2-temp-0cz9j6vy", out_dir="/tmp/qiime2-temp-0cz9j6vy", ncl=1, type=“16S”, which_phenotype=“prevalence”, which_envir=“gut”, dset_column=“dataset”, env_column=“BodySite”, 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-0cz9j6vy")
Loading required package: phylolm
Loading required package: ape
Loading required package: settings
Loading required package: Matrix
Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
:heavy_check_mark: ggplot2 3.2.1 :heavy_check_mark: purrr 0.3.3
:heavy_check_mark: tibble 2.1.3 :heavy_check_mark: dplyr 0.8.3
:heavy_check_mark: tidyr 1.0.0 :heavy_check_mark: stringr 1.4.0
:heavy_check_mark: readr 1.3.1 :heavy_check_mark: forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
:heavy_multiplication_x: tidyr::expand() masks Matrix::expand()
:heavy_multiplication_x: dplyr::filter() masks stats::filter()
:heavy_multiplication_x: dplyr::lag() masks stats::lag()
:heavy_multiplication_x: tidyr::pack() masks Matrix::pack()
:heavy_multiplication_x: tidyr::unpack() masks Matrix::unpack()
Loading required package: ggtree
ggtree v1.14.6 For help: https://guangchuangyu.github.io/software/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
phylogenize graphics stats methods grDevices
[1,] “phylogenize” “phylogenize” “phylogenize” “phylogenize” “phylogenize”
[2,] “furrr” “furrr” “furrr” “furrr” “furrr”
[3,] “future” “future” “future” “future” “future”
[4,] “functional” “functional” “functional” “functional” “functional”
[5,] “biomformat” “biomformat” “biomformat” “biomformat” “biomformat”
[6,] “ggtree” “ggtree” “ggtree” “ggtree” “ggtree”
[7,] “forcats” “forcats” “forcats” “forcats” “forcats”
[8,] “stringr” “stringr” “stringr” “stringr” “stringr”
[9,] “dplyr” “dplyr” “dplyr” “dplyr” “dplyr”
[10,] “purrr” “purrr” “purrr” “purrr” “purrr”
[11,] “readr” “readr” “readr” “readr” “readr”
[12,] “tidyr” “tidyr” “tidyr” “tidyr” “tidyr”
[13,] “tibble” “tibble” “tibble” “tibble” “tibble”
[14,] “ggplot2” “ggplot2” “ggplot2” “ggplot2” “ggplot2”
[15,] “tidyverse” “tidyverse” “tidyverse” “tidyverse” “tidyverse”
[16,] “Matrix” “Matrix” “Matrix” “Matrix” “Matrix”
[17,] “settings” “settings” “settings” “settings” “settings”
[18,] “phylolm” “phylolm” “phylolm” “phylolm” “phylolm”
[19,] “ape” “ape” “ape” “ape” “ape”
[20,] “stats” “stats” “stats” “stats” “stats”
[21,] “graphics” “graphics” “graphics” “graphics” “graphics”
[22,] “grDevices” “grDevices” “grDevices” “grDevices” “grDevices”
[23,] “utils” “utils” “utils” “utils” “utils”
[24,] “datasets” “datasets” “datasets” “datasets” “datasets”
[25,] “methods” “methods” “methods” “methods” “methods”
[26,] “base” “base” “base” “base” “base”
biomformat
[1,] “phylogenize”
[2,] “furrr”
[3,] “future”
[4,] “functional”
[5,] “biomformat”
[6,] “ggtree”
[7,] “forcats”
[8,] “stringr”
[9,] “dplyr”
[10,] “purrr”
[11,] “readr”
[12,] “tidyr”
[13,] “tibble”
[14,] “ggplot2”
[15,] “tidyverse”
[16,] “Matrix”
[17,] “settings”
[18,] “phylolm”
[19,] “ape”
[20,] “stats”
[21,] “graphics”
[22,] “grDevices”
[23,] “utils”
[24,] “datasets”
[25,] “methods”
[26,] “base”
ncl: 1
type: 16S
out_dir: /tmp/qiime2-temp-0cz9j6vy
in_dir: /tmp/qiime2-temp-0cz9j6vy
data_dir: /root/miniconda3/envs/qiime2-2019.4/lib/R/library/phylogenize/extdata
abundance_file: test-abundance.tab
metadata_file: test-metadata.tab
biom_file: input.biom
input_format: biom
separate_metadata: FALSE
env_column: BodySite
dset_column: dataset
sample_column: #SampleID
phenotype_file:
db_version: midas_v1.2
which_phenotype: prevalence
which_envir: gut
prior_type: uninformative
prior_file:
minimum: 3
treemin: 5
pctmin: 0.025
assume_below_LOD: TRUE
skip_graphs: FALSE
burst_dir: /root/miniconda3/pkgs/burst-v0.99.8-0/bin
linearize: FALSE
pryr: FALSE
prev_color_low: black
prev_color_high: orange2
spec_color_low: slateblue
spec_color_mid: gray50
spec_color_high: tomato
gene_color_absent: black
gene_color_present: slateblue2
separate_process: TRUE
biom_dir: /usr/local/bin/
error_to_file: TRUE
burst_16sfile: 16s_renamed.frn
burst_infile: input_seqs.txt
burst_outfile: output_assignments.txt
burst_cutoff: 0.985
burst_bin: burst12
use_rmd_params: FALSE
devel: FALSE
devel_pkgdir: package/phylogenize
relative_out_dir: .
single_dset: TRUE
working_dir: /data/leo/Influentdilutions/qiime2_ tutorial/deblur_test/deblur_250/q2-phylogenize/q2-phylogenize
meas_err: TRUE
min_fx: 0

processing file: phylogenize-report.Rmd
|… | 5%
ordinary text without R code

|… | 9%
label: setup (with options)
List of 5
warning: logi FALSE message: logi FALSE
results: chr "hide" echo : logi FALSE
$ cache : logi TRUE

looking for file: /tmp/qiime2-temp-0cz9j6vy/input.biom
located biom file: /tmp/qiime2-temp-0cz9j6vy/input.biom
Calling BURST with arguments: -r /root/miniconda3/envs/qiime2-2019.4/lib/R/library/phylogenize/extdata/16s_renamed.frn -fr -q /tmp/qiime2-temp-0cz9j6vy/input_seqs.txt -i 0.985 -o /tmp/qiime2-temp-0cz9j6vy/output_assignments.txt
This is BURST [v0.99.8 special edition [PT2.5]]
Hotloading is disabled
–> Also considering the reverse complement of reads
–> Setting identity threshold to 0.985000
Using up to AVX-128 with 32 threads.
Parsed 770 queries (0.033637). Calculating minMax…
Found min 120, max 120 (0.004653).
Converting queries… Converted (0.004589)
Copying queries… Copied (0.004616)
Sorting queries… Sorted (0.227566)
Copying indices… Copied (0.000092)
Determining uniqueness… Done (0.000088). Number unique: 770
Collecting unique sequences… Done (0.000077)
Creating data structures… Done (0.000074) [maxED: 1]
Processing reverse complements… Processed (0.000198) [offset 93170 / 93170]
Re-sorting… Re-sorted (0.214710)
Calculating divergence… Calculated (0.000068) [31.609091 avg div; 120 max]
Parsed 99573 references.
There are 99573 references and hence 6223 clumps (+1)
Average R pack length = 1160.781009
Fingerprints not enabled
Searching best paths through 1540 unique queries…
Search Progress: [100.00%]
Search complete. Consolidating results…
Constructing RefMap…
CAPITALIST: Processed 40291 investments

Alignment time: 15.425737 seconds
4 non-singleton environment(s) found
1 non-singleton dataset(s) found
0.000000000.000000000.082326280.047717840.033717830.000000000.141434260.055555560.000000000.000000000.023880600.000000000.000000000.060240960.000000000.387096770.000000000.000000000.00000000
Starting evaluation…
|… | 14%
inline R code fragments

|… | 18%
label: calculate_phenotype (with options)
List of 7
fig.width : num 7 fig.height: num 20
warning : logi FALSE message : logi FALSE
results : chr "hide" echo : logi FALSE
$ cache : logi TRUE

getting continuous trait ancestry
getting continuous trait ancestry
getting continuous trait ancestry
getting continuous trait ancestry
getting continuous trait ancestry
getting continuous trait ancestry
|… | 23%
ordinary text without R code

|… | 27%
label: plot_pheno_trees (with options)
List of 12
fig.width : num 7 fig.height : num 20
warning : logi FALSE message : logi FALSE
results : chr "hide" echo : logi FALSE
fig.keep : chr "none" fig.ext : chr “svg”
custom.plot: logi TRUE fig.num : language length(plotted.pheno.trees)
cache.lazy : logi FALSE cache : logi TRUE

*** Error in `/root/miniconda3/envs/qiime2-2019.4/lib/R/bin/exec/R’: corrupted size vs. prev_size: 0x00005580692eb910 ***
Traceback (most recent call last):
File “/root/miniconda3/envs/qiime2-2019.4/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 “/root/miniconda3/envs/qiime2-2019.4/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="/root/miniconda3/pkgs/burst-v0.99.8-0/bin/", in_dir="/tmp/qiime2-temp-0cz9j6vy", out_dir="/tmp/qiime2-temp-0cz9j6vy", ncl=1, type=“16S”, which_phenotype=“prevalence”, which_envir=“gut”, dset_column=“dataset”, env_column=“BodySite”, 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-0cz9j6vy")’]’ died with <Signals.SIGABRT: 6>.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-474>”, line 2, in run
File “/root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 427, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.py”, line 41, in run
report_file=“phylogenize-report.Rmd”)
File “/root/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_phylogenize-0+untagged.17.g4354584.dirty-py3.6.egg/q2_phylogenize/_phylogenize.py”, line 152, in _run
raise Exception(“Error %d in R code!” % e.returncode)
Exception: Error -6 in R code!

Plugin error from phylogenize:

Error -6 in R code!

See above for debug info.

I think it is a problem in R, but not sure how to solve the problem in Qiime2.

Thanks

Pinging @pbradz - can you lend a hand here? Thanks!

Thanks @thermokarst!

@afnsul, sorry you’re having trouble. There is no C/C++ code in phylogenize, and this error message (I believe) indicates a bug in C++ code relating to memory management, so I think you’re right that this would have to be a bug either in R (unlikely) or in some C++ code that an R package is calling (much more likely).

Can you provide a little more information about your installation? It would be helpful to know your OS and its version, as well as whether you are running QIIME in the VM or in the conda environment. If you open a fresh R session manually in the same environment and then type:

library(phylogenize)
sessionInfo()

…you should get a detailed list of what versions of which packages are installed.

As a workaround for now, you may also be able to set the option skip_graphs=TRUE to skip drawing the interactive trees, which looks like the part of phylogenize that’s crashing. However, I didn’t expose that option in the QIIME2 plugin, so you would have to run phylogenize manually from within R using render.report() (the README.md in https://bitbucket.org/pbradz/phylogenize should tell you how to do that). This is more cumbersome but would at least allow you to get the analysis running.