Plugin error from demux: [Errno 13] Permission denied: but I do have access to the temp folder

Dear developers,

I’ve encountered the dreaded Error 13.
I’m trying to analyze some data on a server I hadn’t worked on before, and came across the error. So I decided to run the moving pictures tutorial (just in case). Same problem.
I’ll try to be thorough:

This is a conda installation of qiime2-2020.11, no issues came up during install.

conda activate qiime2-2020.11
qiime info
System versions
Python version: 3.6.12
QIIME 2 release: 2020.11
QIIME 2 version: 2020.11.1
q2cli version: 2020.11.1

Installed plugins
alignment: 2020.11.1
composition: 2020.11.1
cutadapt: 2020.11.1
dada2: 2020.11.1
deblur: 2020.11.1
demux: 2020.11.1
diversity: 2020.11.1
diversity-lib: 2020.11.1
emperor: 2020.11.1
feature-classifier: 2020.11.1
feature-table: 2020.11.1
fragment-insertion: 2020.11.1
gneiss: 2020.11.1
longitudinal: 2020.11.1
metadata: 2020.11.1
phylogeny: 2020.11.1
quality-control: 2020.11.1
quality-filter: 2020.11.1
sample-classifier: 2020.11.1
taxa: 2020.11.1
types: 2020.11.1
vsearch: 2020.11.1
Application config directory
/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/var/q2cli
Getting help
To get help with QIIME 2, visit https://qiime2.org

I’m pasting the ‘conda list’ and ‘env’ outputs at the end of this email.

The offending command:

qiime demux emp-single --i-seqs emp-single-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-column barcode-sequence --o-per-sample-sequences demux.qza --o-error-correction-details demux-details.qza --verbose

Error message:
qiime demux emp-single --i-seqs emp-single-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-column barcode-sequence --o-per-sample-sequences demux.qza --o-error-correction-details demux-details.qza --verbose
Traceback (most recent call last):
File “/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in emp_single
File “/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 220, in bound_callable
provenance.add_input(name, artifact)
File “/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/provenance.py”, line 413, in add_input
self.inputs[name] = self.add_ancestor(input)
File “/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/archive/provenance.py”, line 167, in add_ancestor
ignore=shutil.ignore_patterns(self.ANCESTOR_DIR + ‘*’))
File “/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/python3.6/shutil.py”, line 365, in copytree
raise Error(errors)
shutil.Error: [(’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/VERSION’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/VERSION’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/VERSION’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/citations.bib’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/citations.bib’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/citations.bib’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/metadata.yaml’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/metadata.yaml’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/metadata.yaml’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/action/action.yaml’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action/action.yaml’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action/action.yaml’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/action’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4’”)]

Plugin error from demux:

[(’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/VERSION’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/VERSION’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/VERSION’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/citations.bib’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/citations.bib’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/citations.bib’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/metadata.yaml’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/metadata.yaml’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/metadata.yaml’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/action/action.yaml’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action/action.yaml’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action/action.yaml’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance/action’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/action’”), (’/home/iaf/christian.hoffmann/tmp/qiime2-archive-79ptgaqg/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4/provenance’, ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4’, “[Errno 13] Permission denied: ‘/home/iaf/christian.hoffmann/tmp/qiime2-provenance-2snb7nho/artifacts/ee1ec9ab-c72e-4b0b-ab68-63ef65688da4’”)]

See above for debug info.

My temp folder:

echo $TMPDIR/
/home/iaf/christian.hoffmann/tmp/

which has permissions set to 777, so it can be written to by anyone (just in case again).

I came across this topic:


Some issue with python 3.6 and NFS file systems, this is what I have as far as file system:

df -Th /home/iaf/christian.hoffmann/
Filesystem Type Size Used Avail Use% Mounted on
home gpfs 388T 263T 126T 68% /home

I ran out of ideas to test, hence this posting. Any help here is greatly appreciated!
If you need any other info, just let me know.

best,
Chris

conda list

packages in environment at /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
arb-bio-tools 6.0.6 haa8b8d8_8 bioconda
argon2-cffi 20.1.0 py36h1d69622_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
bibtexparser 1.1.0 py_0 conda-forge
binutils_impl_linux-64 2.35.1 h193b22a_1 conda-forge
binutils_linux-64 2.35 hc3fd857_29 conda-forge
bioconductor-biobase 2.50.0 r40h037d062_0 bioconda
bioconductor-biocgenerics 0.36.0 r40_0 bioconda
bioconductor-biocparallel 1.24.0 r40h5f743cb_0 bioconda
bioconductor-biostrings 2.58.0 r40h037d062_0 bioconda
bioconductor-dada2 1.18.0 r40h5f743cb_0 bioconda
bioconductor-delayedarray 0.16.0 r40h037d062_0 bioconda
bioconductor-genomeinfodb 1.26.0 r40_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40_0 bioconda
bioconductor-genomicalignments 1.26.0 r40h037d062_0 bioconda
bioconductor-genomicranges 1.42.0 r40h037d062_0 bioconda
bioconductor-iranges 2.24.0 r40h037d062_0 bioconda
bioconductor-matrixgenerics 1.2.0 r40_0 bioconda
bioconductor-rhtslib 1.22.0 r40h037d062_0 bioconda
bioconductor-rsamtools 2.6.0 r40h5f743cb_0 bioconda
bioconductor-s4vectors 0.28.0 r40h037d062_0 bioconda
bioconductor-shortread 1.48.0 r40h5f743cb_0 bioconda
bioconductor-summarizedexperiment 1.20.0 r40_0 bioconda
bioconductor-xvector 0.30.0 r40h037d062_0 bioconda
bioconductor-zlibbioc 1.36.0 r40h037d062_0 bioconda
biom-format 2.1.10 py36ha112f06_0 conda-forge
blas 2.17 openblas conda-forge
blast 2.10.1 pl526he19e7b1_3 bioconda
bleach 3.2.1 pyh9f0ad1d_0 conda-forge
bokeh 2.2.3 py36h5fab9bb_0 conda-forge
boost-cpp 1.70.0 h7b93d67_3 conda-forge
bowtie2 2.4.2 py36h5202f60_1 bioconda
brotlipy 0.7.0 py36he6145b8_1001 conda-forge
bwidget 1.9.14 ha770c72_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
cachecontrol 0.12.6 py_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
certifi 2020.12.5 py36h5fab9bb_0 conda-forge
cffi 1.14.4 py36hc120d54_1 conda-forge
chardet 3.0.4 py36h9880bd3_1008 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cryptography 3.3.1 py36h0a59100_0 conda-forge
curl 7.71.1 he644dc0_8 conda-forge
cutadapt 3.1 py36h4c5857e_0 bioconda
cycler 0.10.0 py_2 conda-forge
cython 0.29.21 py36ha357f81_1 conda-forge
deblur 1.1.0 py_2 bioconda
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
dendropy 4.5.1 pyh3252c3a_0 bioconda
dnaio 0.4.4 py36h4c5857e_0 bioconda
emperor 1.0.1 py36h5fab9bb_1 conda-forge
entrez-direct 13.9 pl526h375a9b1_0 bioconda
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fastcluster 1.1.26 py36h7c3b610_2 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.13.1 h7e3eb15_1002 conda-forge
freetype 2.10.4 h7ca028e_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py36h5fab9bb_2 conda-forge
gcc_impl_linux-64 7.5.0 hd9e1a51_17 conda-forge
gcc_linux-64 7.5.0 he2a3fca_29 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gfortran_impl_linux-64 7.5.0 hfca37b7_17 conda-forge
gfortran_linux-64 7.5.0 ha081f1e_29 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glib 2.66.3 h9c3ff4c_1 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_1 conda-forge
gxx_impl_linux-64 7.5.0 h7ea4de1_17 conda-forge
gxx_linux-64 7.5.0 h547f3ba_29 conda-forge
h5py 2.10.0 nompi_py36h513d04c_102 conda-forge
harfbuzz 2.7.2 ha5b49bf_1 conda-forge
hdf5 1.10.5 nompi_h7c3c948_1111 conda-forge
hdmedians 0.14.1 py36h68bb277_1 conda-forge
hmmer 3.1b2 3 bioconda
htslib 1.11 hd3b49d5_1 bioconda
icu 67.1 he1b5a44_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 3.1.1 pyhd8ed1ab_0 conda-forge
importlib_metadata 3.1.1 hd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 5.3.4 py36he448a4c_1 conda-forge
ipython 7.16.1 py36he448a4c_2 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 pyh9f0ad1d_1 conda-forge
iqtree 2.0.3 h176a8bc_1 bioconda
isa-l 2.30.0 h36c2ea0_0 conda-forge
jedi 0.17.2 py36h5fab9bb_1 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.17.0 py_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 3.2.0 py_2 conda-forge
jupyter_client 6.1.7 py_0 conda-forge
jupyter_core 4.7.0 py36h5fab9bb_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
kiwisolver 1.3.1 py36h51d7077_0 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_1 conda-forge
libarbdb 6.0.6 haa8b8d8_8 bioconda
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libdeflate 1.6 h516909a_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 7.5.0 h42c25f5_17 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 7.5.0 hae1eefd_17 conda-forge
libgfortran4 7.5.0 hae1eefd_17 conda-forge
libglib 2.66.3 h1f3bc88_1 conda-forge
libgomp 9.3.0 h5dbcf3e_17 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 17_openblas conda-forge
liblapacke 3.8.0 17_openblas conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.10 pthreads_hb3c22a3_5 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-devel_linux-64 7.5.0 h4084dd6_17 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
llvm-openmp 11.0.0 hfc4b9b4_1 conda-forge
lockfile 0.12.2 py_1 conda-forge
lz4 3.1.1 py36hbb6ea5d_0 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
mafft 7.475 h516909a_0 bioconda
make 4.3 hd18ef5c_1 conda-forge
markupsafe 1.1.1 py36he6145b8_2 conda-forge
matplotlib 3.2.2 1 conda-forge
matplotlib-base 3.2.2 py36h5fdd944_1 conda-forge
mistune 0.8.4 py36h1d69622_1002 conda-forge
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.0 py36h51d7077_2 conda-forge
natsort 7.1.0 pyhd8ed1ab_0 conda-forge
nbclient 0.5.1 py_0 conda-forge
nbconvert 6.0.7 py36h5fab9bb_3 conda-forge
nbformat 5.0.8 py_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge
networkx 2.5 py_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.1.5 py36h5fab9bb_0 conda-forge
numpy 1.19.4 py36h2aa4a07_2 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjdk 11.0.8 hacce0ff_0 conda-forge
openssl 1.1.1h h516909a_0 conda-forge
packaging 20.7 pyhd3deb0d_0 conda-forge
pandas 1.1.5 py36h284efc9_0 conda-forge
pandoc 2.11.2 h36c2ea0_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
parso 0.7.1 pyh9f0ad1d_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pcre2 10.35 h032f7d1_2 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.04 pl526_0 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
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NM=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-nm
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CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
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LANG=en_US.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
LOADEDMODULES=
DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
F77=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-gfortran
PS1=(qiime2-2020.11) [\e[32m][[\e[m][\e[31m]\u[\e[m][\e[33m]@[\e[m][\e[32m]\h[\e[m]:[\e[36m]\w[\e[m][\e[32m]][\e[m][\e[32;47m]$[\e[m]
SELINUX_LEVEL_REQUESTED=
CENTRIFUGE_BASE=/home/iaf/christian.hoffmann/tools/centrifuge
CXX=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-c++
CC_FOR_BUILD=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-cc
_CE_M=
HISTCONTROL=ignoredups
KRB5CCNAME=KEYRING:persistent:140069
OBJCOPY=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-objcopy
SHLVL=1
HOME=/home/iaf/christian.hoffmann
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
FC=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-gfortran
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
GCC=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-gcc
ADDR2LINE=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/iaf/christian.hoffmann/miniconda3/bin/python
TMP=/home/iaf/christian.hoffmann/tmp
LOGNAME=christian.hoffmann
build_alias=x86_64-conda-linux-gnu
SSH_CONNECTION=146.107.184.42 64058 146.107.1.224 22
MODULESHOME=/usr/share/Modules
JAVA_HOME_CONDA_BACKUP=
CONDA_DEFAULT_ENV=qiime2-2020.11
LESSOPEN=||/usr/bin/lesspipe.sh %s
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
RANLIB=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-ranlib
CMAKE_PREFIX_PATH=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11:/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/x86_64-conda-linux-gnu/sysroot/usr
CC=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-cc
XDG_RUNTIME_DIR=/run/user/140069
host_alias=x86_64-conda-linux-gnu
READELF=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-readelf
JAVA_LD_LIBRARY_PATH_BACKUP=
GCC_AR=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-gcc-ar
OBJDUMP=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-objdump
R_LIBS_USER=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/lib/R/library/
GPROF=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-gprof
GXX=/home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/bin/x86_64-conda-linux-gnu-g++
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/qiime2-2020.11/include
BASH_FUNC_module()=() { eval /usr/bin/modulecmd bash $*
}
_=/usr/bin/env

1 Like

Hi @ecohoffmann and welcome to the forum! :wave:

Thanks so much for the very thorough report. :pray:

My guess is that you may be running up against a storage quota. :floppy_disk: Am I right that you are running this on a remote cluster? HPC clusters often have storage quotas on various locations in the filesystem, including a users home directory. I would suggest setting your temporary directory (I see both TEMPDIR and TEMP in your environment but I’m not sure which one is being used) to another location that you are sure has sufficient disk space available. Let me know if that helps. If not we will take a deeper look!

1 Like

Hello @andrewsanchez,

Thanks for reply.
It is a HPC cluster, and qiime2 is using $TMPDIR.
I think I have overcome this issue, for now, so I will post the solution here for reference.

It was not the quota (the post I linked on opening suggested it could be that).
I have plenty of space and I have tested cleaning out the $TMPDIR folder I was using (which in fairness was pretty full).
No luck there.
I tried using other locations in the clusters.
One is where we are keeping our sequencing runs, so plenty of space as well. No luck there either.

But I had luck on a top level tmp folder (/tmp).

The difference, as far as I can tell, and following the NFS lead on that posting I linked on opening the topic, has to do with the FS (major guess here… I’m definitely not a systems guru).
But, here is the info for where it worked and were it didn’t:

Didn’t work here:
$TMPDIR=/home/iaf/christian.hoffmann/tmp
$TMPDIR=/project/sequencing/IAF/temp

df -Th /project/sequencing/IAF/temp
Filesystem Type Size Used Avail Use% Mounted on
project gpfs 431T 156T 275T 37% /project

df -Th /home/iaf/christian.hoffmann/
Filesystem Type Size Used Avail Use% Mounted on
home gpfs 388T 266T 123T 69% /home

Both are gpfs types.

It worked here:

df -Th /tmp/
Filesystem Type Size Used Avail Use% Mounted on
/dev/mapper/myvg-rootvol xfs 215G 9.7G 206G 5% /

Here it is xfs type.

For now things are working.
I’m setting my qiime2 conda env to have this location as a $TMPDIR when it activates, and I’ll complete testing things with moving pictures tutorial (just in case), and if I find any other issues related to this error I’ll bring them up here.

Thanks for the help!
Chris

3 Likes

Glad you got everything working, and thank you so much for sharing your results!

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