plugin error from feature-table on server

I’m trying to convert qza formatted table to qzv formatted table using qiime feature-table summarize.
Whenever I try it, I get an error.

qiime feature-table summarize --i-table table-dn-97.qza --o-visualization table-dn-97.qzv --m-sample-metadata-file Fasting_Map.txt

Plugin error from feature-table:
[Errno 22] Invalid argument: ‘/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2templates/templates/tab-parent.html’

Debug info has been saved to /tmp/qiime2-q2cli-err-4_bv2o9c.log

Please help me.

ps. I’m working it on the server (CentOS 7).

Hi @Kyu-Chan_Lee,

Could you provide the full contents of the log file to help debug?

Thanks,
Justine

1 Like

Hi, Justine
Here my full contents of log!!

Traceback (most recent call last):
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/decorator.py:decorator-gen-321>”, line 2, in summarize
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/meta/miniconda3/envs/qiime2/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 “/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py”, line 146, in summarize
q2templates.render(templates, output_dir, context=context)
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2templates/_templates.py”, line 48, in render
temp_dir.name)
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/shutil.py”, line 258, in copy2
copystat(src, dst, follow_symlinks=follow_symlinks)
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/shutil.py”, line 225, in copystat
_copyxattr(src, dst, follow_symlinks=follow)
File “/home/meta/miniconda3/envs/qiime2/lib/python3.6/shutil.py”, line 164, in _copyxattr
value = os.getxattr(src, name, follow_symlinks=follow_symlinks)
OSError: [Errno 22] Invalid argument: ‘/home/meta/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2templates/templates/tab-parent.html’

Thank you,
Kyu-Chan

Hi @Kyu-Chan_Lee, this looks like an incomplete conda environment. Are you able to remove the environment and then re-install from scratch? If yes, then I suggest doing that. If no (for example, on a shared cluster), please activate the environment, then run conda list and return the results here - thanks! :t_rex:

2 Likes

Hi, @thermokarst,

I re-installed conda (this time anaconda) and qiime2, but the same error comes out.

When I tried to install qiime2, q2templates, q2-deblur and q2-fragment-insertion packages were not installed.
So I installed q2templates with this command, conda install -c qiime2/label/r2019.1 q2templates.
q2-deblur and q2-fragment-insertion were not installed with this kind of commands, I input the same installation command (conda env create -n ~~~) as I used before.
It seemed that q2-deblur and q2-fragment-insertion packages were successfully installed.
However, I got the same error.

As you said, I attached the results of conda list

packages in environment at /home/meta/anaconda3/envs/qiime2:

Name Version Build Channel

_r-mutex 1.0.0 anacondar_1
arb-bio-tools 6.0.6 h5901010_6 bioconda
asn1crypto 0.24.0 py36_1003 conda-forge
atk 2.25.90 hf2eb9ee_1001 conda-forge
atomicwrites 1.2.1 py_0 conda-forge
attrs 18.2.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bibtexparser 1.1.0 py_0 conda-forge
bioconductor-biobase 2.38.0 r341h219a75b_1 bioconda
bioconductor-biocgenerics 0.24.0 r341_1 bioconda
bioconductor-biocparallel 1.12.0 r341h219a75b_1 bioconda
bioconductor-biostrings 2.46.0 r3.4.1_0 bioconda
bioconductor-dada2 1.6.0 r3.4.1_0 bioconda
bioconductor-delayedarray 0.4.1 r3.4.1_0 bioconda
bioconductor-genomeinfodb 1.14.0 r3.4.1_0 bioconda
bioconductor-genomeinfodbdata 1.0.0 r3.4.1_1 bioconda
bioconductor-genomicalignments 1.14.1 r3.4.1_0 bioconda
bioconductor-genomicranges 1.30.3 r3.4.1_0 bioconda
bioconductor-iranges 2.12.0 r3.4.1_0 bioconda
bioconductor-rsamtools 1.30.0 r3.4.1_0 bioconda
bioconductor-s4vectors 0.16.0 r3.4.1_0 bioconda
bioconductor-shortread 1.36.0 r3.4.1_0 bioconda
bioconductor-summarizedexperiment 1.8.0 r3.4.1_0 bioconda
bioconductor-xvector 0.18.0 r3.4.1_0 bioconda
bioconductor-zlibbioc 1.24.0 r3.4.1_0 bioconda
biom-format 2.1.7 py36h3010b51_1002 conda-forge
blas 1.0 mkl
blast 2.7.1 h4422958_6 bioconda
bleach 3.1.0 py_0 conda-forge
bokeh 1.0.4 py36_1000 conda-forge
boost 1.67.0 py36h3e44d54_0 conda-forge
boost-cpp 1.67.0 h3a22d5f_0 conda-forge
bz2file 0.98 py_0 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2019.1.23 0
cachecontrol 0.12.5 py_0 conda-forge
cairo 1.14.12 h80bd089_1005 conda-forge
certifi 2019.3.9 py36_0
cffi 1.11.5 py36h9745a5d_1001 conda-forge
chardet 3.0.4 py36_1003 conda-forge
click 7.0 py_0 conda-forge
cryptography 2.3.1 py36hb7f436b_1000 conda-forge
curl 7.61.0 h93b3f91_2 conda-forge
cutadapt 1.18 py36h14c3975_1 bioconda
cycler 0.10.0 py_1 conda-forge
dbus 1.13.0 h4e0c4b3_1000 conda-forge
deblur 1.1.0 py36_0 bioconda
decorator 4.3.2 py_0 conda-forge
emperor 1.0.0beta18 py36_1001 conda-forge
entrypoints 0.3 py36_1000 conda-forge
expat 2.2.5 hf484d3e_1002 conda-forge
fastcluster 1.1.25 py36h637b7d7_1000 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.9.1 h94bbf69_1005 conda-forge
future 0.17.1 py36_1000 conda-forge
gdk-pixbuf 2.36.12 h4f1c04b_1001 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.56.2 had28632_1001 conda-forge
gmp 6.1.2 hf484d3e_1000 conda-forge
gneiss 0.4.4 py_0 bioconda
gnutls 3.5.19 h2a4e5f8_1 conda-forge
gobject-introspection 1.56.1 py36h9e29830_1001 conda-forge
graphite2 1.3.13 hf484d3e_1000 conda-forge
gsl 2.2.1 h0c605f7_3
gstreamer 1.12.5 h0cc0488_1000 conda-forge
gtk2 2.24.31 h5baeb44_1000 conda-forge
h5py 2.9.0 nompi_py36hf008753_1102 conda-forge
harfbuzz 1.9.0 he243708_1001 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
hdmedians 0.13 py36h3010b51_1000 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py36_1000 conda-forge
ijson 2.3 py_1 conda-forge
intel-openmp 2019.1 144
ipykernel 5.1.0 py36h24bf2e0_1002 conda-forge
ipython 7.2.0 py36h24bf2e0_1000 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
iqtree 1.6.9 he860b03_1 bioconda
jedi 0.13.2 py36_1000 conda-forge
jinja2 2.10.1 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.0.0a3 py36_1000 conda-forge
jupyter_client 5.2.4 py_3 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.0.1 py36h6bb024c_1002 conda-forge
krb5 1.14.6 0 conda-forge
libarbdb 6.0.6 h5901010_6 bioconda
libcurl 7.61.1 heec0ca6_0
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.3.0 hdf63c60_0
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3
libiconv 1.15 h516909a_1005 conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libsodium 1.0.16 h14c3975_1001 conda-forge
libssh2 1.8.0 h1ad7b7a_1003 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0
libtiff 4.0.10 h9022e91_1002 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
lockfile 0.12.2 py_1 conda-forge
mafft 7.310 1 bioconda
markupsafe 1.1.0 py36h14c3975_1000 conda-forge
matplotlib 3.0.2 py36_1002 conda-forge
matplotlib-base 3.0.2 py36h167e16e_1002 conda-forge
mistune 0.8.4 py36h14c3975_1000 conda-forge
mkl 2019.1 144
mkl_fft 1.0.10 py36h14c3975_1 conda-forge
mkl_random 1.0.2 py36h637b7d7_2 conda-forge
more-itertools 4.3.0 py36_1000 conda-forge
msgpack-python 0.6.1 py36h6bb024c_0 conda-forge
natsort 5.5.0 py_0 conda-forge
nbconvert 5.3.1 py36_0
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nettle 3.3 0 conda-forge
nose 1.3.7 py36_1002 conda-forge
notebook 5.7.4 py36_1 conda-forge
numpy 1.15.4 py36h7e9f1db_0
numpy-base 1.15.4 py36hde5b4d6_0
olefile 0.46 py_0 conda-forge
openjdk 11.0.1 h516909a_1015 conda-forge
openssl 1.0.2r h7b6447c_0
packaging 19.0 py_0 conda-forge
pandas 0.23.4 py36h637b7d7_1000 conda-forge
pandoc 2.5 1 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.40.14 hf0c64fd_1003 conda-forge
parso 0.3.2 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.41 hf484d3e_1003 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
perl-archive-tar 2.32 pl526_0 bioconda
perl-carp 1.38 pl526_2 bioconda
perl-compress-raw-bzip2 2.084 pl526hfc679d8_0 bioconda
perl-compress-raw-zlib 2.084 pl526h6bb024c_1 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.34 pl526_3 bioconda
perl-io-compress 2.084 pl526hfc679d8_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-pathtools 3.73 h470a237_2 bioconda
perl-scalar-list-utils 1.45 pl526h470a237_3 bioconda
perl-test-more 1.001002 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
pexpect 4.6.0 py36_1000 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pigz 2.3.4 0 conda-forge
pillow 5.4.1 py36h00a061d_1000 conda-forge
pip 19.0.1 py36_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
pluggy 0.8.1 py_0 conda-forge
prometheus_client 0.5.0 py_0 conda-forge
prompt_toolkit 2.0.8 py_0 conda-forge
psutil 5.4.8 py36h14c3975_1000 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.7.0 py_0 conda-forge
pycparser 2.19 py36_1 conda-forge
pygments 2.3.1 py_0 conda-forge
pyopenssl 18.0.0 py36_1000 conda-forge
pyparsing 2.3.0 py_0 conda-forge
pyqt 5.6.0 py36h13b7fb3_1008 conda-forge
pyrsistent 0.14.9 py36h14c3975_1000 conda-forge
pysocks 1.6.8 py36_1002 conda-forge
pytest 4.1.1 py36_1000 conda-forge
python 3.6.7 hd21baee_1002 conda-forge
python-dateutil 2.7.5 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
pyyaml 3.13 py36h14c3975_1001 conda-forge
pyzmq 17.1.2 py36h6afc9c9_1001 conda-forge
q2-alignment 2019.1.0 py36_0 qiime2/label/r2019.1
q2-composition 2019.1.0 py36_0 qiime2/label/r2019.1
q2-cutadapt 2019.1.0 py36_0 qiime2/label/r2019.1
q2-dada2 2019.1.0 py36_0 qiime2/label/r2019.1
q2-deblur 2019.1.0 py36_0 qiime2/label/r2019.1
q2-demux 2019.1.0 py36_0 qiime2/label/r2019.1
q2-diversity 2019.1.0 py36_0 qiime2/label/r2019.1
q2-emperor 2019.1.0 py36_0 qiime2/label/r2019.1
q2-feature-classifier 2019.1.0 py36_0 qiime2/label/r2019.1
q2-feature-table 2019.1.0 py36_0 qiime2/label/r2019.1
q2-fragment-insertion 2019.1.0 py36_0 qiime2/label/r2019.1
q2-gneiss 2019.1.0 py36_0 qiime2/label/r2019.1
q2-longitudinal 2019.1.0 py36_0 qiime2/label/r2019.1
q2-metadata 2019.1.0 py36_0 qiime2/label/r2019.1
q2-phylogeny 2019.1.0 py36_0 qiime2/label/r2019.1
q2-quality-control 2019.1.0 py36_0 qiime2/label/r2019.1
q2-quality-filter 2019.1.0 py36_0 qiime2/label/r2019.1
q2-sample-classifier 2019.1.0 py36_0 qiime2/label/r2019.1
q2-taxa 2019.1.0 py36_0 qiime2/label/r2019.1
q2-types 2019.1.0 py36_0 qiime2/label/r2019.1
q2-vsearch 2019.1.0 py36_0 qiime2/label/r2019.1
q2cli 2019.1.0 py36_0 qiime2/label/r2019.1
q2templates 2019.1.0 py36_0 qiime2/label/r2019.1
qiime2 2019.1.0 py36_0 qiime2/label/r2019.1
qt 5.6.2 hbe13537_1012 conda-forge
r-assertthat 0.2.0 r341h6115d3f_1 conda-forge
r-base 3.4.1 h4fe35fd_8 conda-forge
r-bh 1.66.0_1 r341_1001 conda-forge
r-bitops 1.0_6 r341hc070d10_2 conda-forge
r-cli 1.0.0 r341h6115d3f_1 conda-forge
r-cluster 2.0.7_1 r341h364d78e_0 conda-forge
r-colorspace 1.3_2 r341hc070d10_2 conda-forge
r-crayon 1.3.4 r341h6115d3f_1 conda-forge
r-data.table 1.11.4 r341hc070d10_2 conda-forge
r-digest 0.6.18 r341hc070d10_0 conda-forge
r-fansi 0.3.0 r341hc070d10_0 conda-forge
r-formatr 1.5 r341h6115d3f_1 conda-forge
r-futile.logger 1.4.3 r341h6115d3f_1 conda-forge
r-futile.options 1.0.1 r341h6115d3f_0 conda-forge
r-ggplot2 3.1.0 r341h6115d3f_0 conda-forge
r-glue 1.3.0 r341h470a237_2 conda-forge
r-gtable 0.2.0 r341h6115d3f_1 conda-forge
r-hwriter 1.3.2 r341h6115d3f_1 conda-forge
r-labeling 0.3 r341h6115d3f_1 conda-forge
r-lambda.r 1.2.3 r341h6115d3f_0 conda-forge
r-lattice 0.20_35 r341hc070d10_0 conda-forge
r-latticeextra 0.6_28 r341h6115d3f_1 conda-forge
r-lazyeval 0.2.1 r341hc070d10_2 conda-forge
r-magrittr 1.5 r341h6115d3f_1 conda-forge
r-mass 7.3_50 r341hc070d10_2 conda-forge
r-matrix 1.2_14 r341hc070d10_2 conda-forge
r-matrixstats 0.54.0 r341hc070d10_0 conda-forge
r-mgcv 1.8_24 r341hc070d10_2 conda-forge
r-munsell 0.5.0 r341h6115d3f_1 conda-forge
r-nlme 3.1_137 r341h364d78e_0 conda-forge
r-permute 0.9_4 r341_1002 conda-forge
r-pillar 1.3.0 r341h6115d3f_0 conda-forge
r-plyr 1.8.4 r341h9d2a408_2 conda-forge
r-r6 2.2.2 r341h6115d3f_1 conda-forge
r-rcolorbrewer 1.1_2 r341h6115d3f_1 conda-forge
r-rcpp 1.0.0 r341h9d2a408_0 conda-forge
r-rcppparallel 4.4.1 r341h9d2a408_0 conda-forge
r-rcurl 1.95_4.11 r341hc070d10_3 conda-forge
r-reshape2 1.4.3 r341h9d2a408_2 conda-forge
r-rlang 0.3.0.1 r341h470a237_0 conda-forge
r-scales 1.0.0 r341h9d2a408_1 conda-forge
r-snow 0.4_3 r341h6115d3f_0 conda-forge
r-stringi 1.2.4 r341h9d2a408_1 conda-forge
r-stringr 1.3.1 r341h6115d3f_1 conda-forge
r-tibble 1.4.2 r341hc070d10_2 conda-forge
r-utf8 1.1.4 r341hc070d10_0 conda-forge
r-vegan 2.5_3 r341h364d78e_0 conda-forge
r-viridislite 0.3.0 r341h6115d3f_1 conda-forge
r-withr 2.1.2 r341h6115d3f_0 conda-forge
raxml 8.2.12 h14c3975_1 bioconda
readline 7.0 hf8c457e_1001 conda-forge
requests 2.21.0 py36_1000 conda-forge
scikit-bio 0.5.5 py36h3010b51_1000 conda-forge
scikit-learn 0.20.2 py36hd81dba3_0
scipy 1.2.0 py36h7c811a0_0
seaborn 0.9.0 py_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 40.7.1 py36_0 conda-forge
sina 1.4.0 h4ef8376_0 bioconda
sip 4.18.1 py36hf484d3e_1000 conda-forge
six 1.12.0 py36_1000 conda-forge
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.26.0 h67949de_1001 conda-forge
statsmodels 0.9.0 py36h3010b51_1000 conda-forge
tbb 2019.3 h6bb024c_1000 conda-forge
terminado 0.8.1 py36_1001 conda-forge
testpath 0.4.2 py_1001 conda-forge
tk 8.6.9 h84994c4_1001 conda-forge
tornado 5.1.1 py36h14c3975_1000 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
tzlocal 1.5.1 py_0 conda-forge
unifrac 0.9.3 py36h5a278d6_0 bioconda
urllib3 1.24.1 py36_1000 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wget 1.19.5 h1ad7b7a_0
wheel 0.32.3 py36_0 conda-forge
widgetsnbextension 3.4.2 py36_1000 conda-forge
xopen 0.4.1 py_0 bioconda
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h516909a_1004 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.6 h14c3975_1000 conda-forge
xorg-libxau 1.0.8 h14c3975_1006 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h516909a_1004 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.2.5 hf484d3e_1006 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
zstd 1.3.3 1 conda-forge

Thanks!

This is a problem.

How are you installing QIIME 2? Can you please walk me through your steps? Copy and paste commands and their output, please! :cactus:

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