【QIIME2】BUG汇总

dada2

问题

输入命令：

time qiime dada2 denoise-paired \
  --i-demultiplexed-seqs mjsample.qza \
  --p-trunc-len-f 295 \
--p-trunc-len-r 262 \
--p-trim-left-f 25 \
--p-trim-left-r 18 \
--o-representative-sequences rep-seqs.qza \
--o-table table.qza \
--o-denoising-stats stats-dada2.qza \
--p-n-threads 20

报错：

Plugin error from dada2:
  An error was encountered while running DADA2 in R (return code 255), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-5z7d1svd.log

解决方法

env
which R
#####响应
(yancao) yangzy@LAPTOP-G-Pro:/mnt/f/WSL_old/QIIME2/data/2025/data.799F_1193R/rawData$ env
SHELL=/bin/bash
WSL2_GUI_APPS_ENABLED=1
CONDA_EXE=/home/yangzy/anaconda3/bin/conda
_CE_M=
WSL_DISTRO_NAME=Ubuntu
PYTHONNOUSERSITE=/home/yangzy/anaconda3/envs/yancao/lib/python*/site-packages/
JAVA_HOME=/home/yangzy/anaconda3/envs/yancao/lib/jvm
JAVA_LD_LIBRARY_PATH=/home/yangzy/anaconda3/envs/yancao/lib/jvm/lib/server
XML_CATALOG_FILES=file:///home/yangzy/anaconda3/envs/yancao/etc/xml/catalog file:///etc/xml/catalog
NAME=LAPTOP-G-Pro
PWD=/mnt/f/WSL_old/QIIME2/data/2025/data.799F_1193R/rawData
GSETTINGS_SCHEMA_DIR=/home/yangzy/anaconda3/envs/yancao/share/glib-2.0/schemas
LOGNAME=yangzy
CONDA_PREFIX=/home/yangzy/anaconda3/envs/yancao
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
RSTUDIO_WHICH_R=/home/yangzy/anaconda3/envs/yancao/bin/R
MOTD_SHOWN=update-motd
HOME=/home/yangzy
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/11_interop
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
CONDA_PROMPT_MODIFIER=(yancao)
R_LIBS_USER=/home/yangzy/anaconda3/envs/yancao/lib/R/library/
JAVA_LD_LIBRARY_PATH_BACKUP=
LESSCLOSE=/usr/bin/lesspipe %s %s
TERM=xterm-256color
_CE_CONDA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=yangzy
CONDA_SHLVL=2
DISPLAY=:0
SHLVL=1
MPLBACKEND=Agg
CONDA_PYTHON_EXE=/home/yangzy/anaconda3/bin/python
LD_LIBRARY_PATH=/usr/local/cuda-12.3/lib64:
XDG_RUNTIME_DIR=/mnt/wslg/runtime-dir
CONDA_DEFAULT_ENV=yancao
WSLENV=
JAVA_HOME_CONDA_BACKUP=
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
PATH=/mnt/c/Users/yang51/Desktop/lw/COSMO/cosmo0.9:/home/yangzy/anaconda3/envs/yancao/bin:/home/yangzy/anaconda3/condabin:/usr/local/cuda-12.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/WindowsApps/MicrosoftCorporationII.WindowsSubsystemForLinux_2.3.26.0_x64__8wekyb3d8bbwe:/mnt/d/Python313/Scripts:/mnt/d/Python313:/mnt/c/Perl64/site/bin:/mnt/c/Perl64/bin:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/d/Install/MEGA11:/mnt/d/Install/sratoolkit.3.1.1-win64/bin:/mnt/d/anaconda3/Scripts:/mnt/d/R/R-4.4.1/bin:/mnt/d/NCBI/blast-2.16.0+/bin:/mnt/c/Users/yang51/AppData/Local/Microsoft/WindowsApps:/mnt/d/Install/PyCharm Community Edition 2024.2.3/bin:/mnt/d/Install/Microsoft VS Code/bin:/snap/bin
HOSTTYPE=x86_64
CONDA_PREFIX_1=/home/yangzy/anaconda3
PULSE_SERVER=unix:/mnt/wslg/PulseServer
OLDPWD=/mnt/f/WSL_old/QIIME2/data/2025/data.799F_1193R
_=/usr/bin/env
(yancao) yangzy@LAPTOP-G-Pro:/mnt/f/WSL_old/QIIME2/data/2025/data.799F_1193R/rawData$ which R
/home/yangzy/anaconda3/envs/yancao/bin/R

但是实际中并不存在该目录

 cd /home/yangzy/anaconda3/envs/yancao/bin/R
-bash: cd: /home/yangzy/anaconda3/envs/yancao/bin/R: Not a directory

尝试用conda安装R