Dear all,
I'm trying to use Decontam plugin, but I'm still obtaining the same error message:
Plugin error from quality-control:
An error was encountered while running Decontam in R (return code 1), please inspect stdout and stderr to learn more.
I know there is a string on this topic , but it's not sufficient for me.
I'm providing my metadata file, my script and also the whole error message.
Any suggestions??metadata_decontam.tsv (1.1 KB)15_decontam.tsv (745 Bytes)15_decontam_ste_596967.tsv (3.6 KB)
Oddant1
March 22, 2024, 5:33pm
3
Hello @MARTIN_MIHULA , it looks as though your R installation is attempting and failing to load a necessary file. First of all, do you have R installed on that computer outside of a QIIME 2 conda environment? This sometimes causes issues for us because R thinks it knows better than we do what files we should be using (it doesn't).
Second, can you run the following commands both in and out of your environment and post the results here please? echo $PATH, which R, and R --version? Thank you.
Yes, I have! Thank you for very fast answer.
Out of the conda environment:
And inside my environment:
Oddant1
March 25, 2024, 5:04pm
5
You appear to have a conflicting version of R in your base conda environment, can you please do the following 2 things:
Inside of your conda environment run the command R -e 'print(.libPaths())' and post the results here
Please post your .bashrc file here (should be at /home/username/.bashrc) .
Certainly.
R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> print(.libPaths())
[1] "/home/XX/YY/.conda/envs/qiime2-amplicon-2024.2/lib/R/library"
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples
# If not running interactively, don't do anything
case $- in
*i*) ;;
*) return;;
esac
# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth
# append to the history file, don't overwrite it
shopt -s histappend
# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000
# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize
# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar
# make less more friendly for non-text input files, see lesspipe(1)
#[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
debian_chroot=$(cat /etc/debian_chroot)
fi
# set a fancy prompt (non-color, unless we know we "want" color)
:
case "$TERM" in
xterm-color|*-256color) color_prompt=yes;;
esac
# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes
if [ -n "$force_color_prompt" ]; then
if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
# We have color support; assume it's compliant with Ecma-48
# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
# a case would tend to support setf rather than setaf.)
color_prompt=yes
else
color_prompt=
fi
fi
if [ "$color_prompt" = yes ]; then
PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt
# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
;;
*)
;;
esac
# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
alias ls='ls --color=auto'
#alias dir='dir --color=auto'
#alias vdir='vdir --color=auto'
#alias grep='grep --color=auto'
#alias fgrep='fgrep --color=auto'
#alias egrep='egrep --color=auto'
fi
# colored GCC warnings and errors
#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
# some more ls aliases
#alias ll='ls -l'
#alias la='ls -A'
#alias l='ls -CF'
# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi
# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
if [ -f /usr/share/bash-completion/bash_completion ]; then
. /usr/share/bash-completion/bash_completion
elif [ -f /etc/bash_completion ]; then
. /etc/bash_completion
fi
fi
source /etc/profile.d/modules.sh
# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi
# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
if [ -f /usr/share/bash-completion/bash_completion ]; then
. /usr/share/bash-completion/bash_completion
elif [ -f /etc/bash_completion ]; then
. /etc/bash_completion
fi
fi
source /etc/profile.d/modules.sh
module load
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/conda/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/conda/anaconda3/etc/profile.d/conda.sh" ]; then
. "/opt/conda/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/opt/conda/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
(END)
Other information:
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beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
bibtexparser 1.4.1 pyhd8ed1ab_0 conda-forge
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certifi 2024.2.2 py38h06a4308_0
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charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
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r-textshaping 0.3.6 r42hbb20487_4 conda-forge
r-tibble 3.2.1 r42h57805ef_2 conda-forge
r-tidyr 1.3.1 r42ha503ecb_0 conda-forge
r-tidyselect 1.2.0 r42hc72bb7e_1 conda-forge
r-tidytree 0.4.6 r42hc72bb7e_0 conda-forge
r-tidyverse 2.0.0 r42h785f33e_1 conda-forge
r-timechange 0.3.0 r42ha503ecb_0 conda-forge
r-tinytex 0.49 r42hc72bb7e_1 conda-forge
r-tzdb 0.4.0 r42ha503ecb_1 conda-forge
r-utf8 1.2.4 r42h57805ef_0 conda-forge
r-uuid 1.2_0 r42h57805ef_0 conda-forge
r-uwot 0.1.16 r42ha503ecb_0 conda-forge
r-vctrs 0.6.5 r42ha503ecb_0 conda-forge
r-vegan 2.6_4 r42hd9ac46e_1 conda-forge
r-vipor 0.4.7 r42hc72bb7e_0 conda-forge
r-viridis 0.6.5 r42hc72bb7e_0 conda-forge
r-viridislite 0.4.2 r42hc72bb7e_1 conda-forge
r-vroom 1.6.5 r42ha503ecb_0 conda-forge
r-withr 3.0.0 r42hc72bb7e_0 conda-forge
r-xfun 0.42 r42ha503ecb_0 conda-forge
r-xml2 1.3.3 r42h044e5c7_2 conda-forge
r-xtable 1.8_4 r42hc72bb7e_5 conda-forge
r-yaml 2.3.8 r42h57805ef_0 conda-forge
r-yulab.utils 0.1.4 r42hc72bb7e_0 conda-forge
raxml 8.2.13 h031d066_0 bioconda
readline 8.2 h8228510_1 conda-forge
referencing 0.33.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rescript 2024.2.0 py38hbae55e2_0 https://packages.qiime2.org/qiime2/2024.2/amplicon/released
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.18.0 py38h0cc4f7c_0 conda-forge
samtools 1.18 hd87286a_0 bioconda
scikit-bio 0.5.8 py38h7e4f40d_1 conda-forge
scikit-learn 0.24.1 py38h658cfdd_0 conda-forge
scipy 1.10.0 py38h10c12cc_2 conda-forge
seaborn 0.12.2 hd8ed1ab_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
sepp 4.3.10 py38h3252c3a_2 bioconda
setproctitle 1.3.3 py38h01eb140_0 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
simplejson 3.19.2 py38h01eb140_0 conda-forge
sip 6.7.12 py38h17151c0_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
sortmerna 2.0 he860b03_4 bioconda
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.0 py38h7f0c24c_3 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tbb 2021.9.0 hf52228f_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.0 pyh0d859eb_0 conda-forge
threadpoolctl 3.3.0 pyhc1e730c_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h0c5db8f_5 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.12.3 pyha770c72_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py38h01eb140_1 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typeguard 2.13.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.20240106 pyhd8ed1ab_0 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzlocal 2.1 pyh9f0ad1d_0 conda-forge
umap-learn 0.5.5 py38h578d9bd_1 conda-forge
unicodedata2 15.1.0 py38h01eb140_0 conda-forge
unifrac 1.3 py38hbff2b2d_0 bioconda
unifrac-binaries 1.3.2 hb7a8b62_2 bioconda
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 1.26.18 pyhd8ed1ab_0 conda-forge
vsearch 2.22.1 h6a68c12_2 bioconda
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.10 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py38h01eb140_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xkeyboard-config 2.38 h0b41bf4_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xopen 1.9.0 py38h578d9bd_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.3.0 hd590300_0 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yq 3.2.3 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h59595ed_1 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.22.0 py38ha98ab4e_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Oddant1
March 26, 2024, 4:52pm
8
It certainly looks like inside of your conda environment it is using the correct version of R, do you have permission to tear down and recreate your conda environment? Maybe remove it then run a conda clean --all for safety (this will remove cached packages and force you to redownload them) then recreate the environment. I'm not seeing anything unusual in your .bashrc or anything especially given that in your environment you have the correct R.