Unable to open docker instance with Singularity
Opened this issue · 1 comments
Hi Yoshiaki,
After my previous issue with memory requirements and not being able to edit this in the wrapper script (I don't understand Docker very well), now I cannot even seem to use Singularity to run the pipeline through the Docker/Singularity instance as of approximately 2 seconds ago. I don't really understand this error message. My version of Singularity has not changed (Singularity/4.0.1-GCCcore-12.2.0, as a module on my HPC), nor have my versions of Virtus or dependencies:
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
argcomplete 3.1.1 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
cachecontrol 0.13.1 pypi_0 pypi
certifi 2023.5.7 pypi_0 pypi
charset-normalizer 3.1.0 pypi_0 pypi
coloredlogs 15.0.1 pypi_0 pypi
contourpy 1.1.0 pypi_0 pypi
cwl-upgrader 1.2.8 pypi_0 pypi
cwl-utils 0.28 pypi_0 pypi
cwltool 3.1.20231020140205 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
docker 6.1.3 pypi_0 pypi
filelock 3.12.2 pypi_0 pypi
fonttools 4.40.0 pypi_0 pypi
humanfriendly 10.0 pypi_0 pypi
idna 3.4 pypi_0 pypi
importlib-resources 5.12.0 pypi_0 pypi
isodate 0.6.1 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 4.9.2 pypi_0 pypi
matplotlib 3.7.1 pypi_0 pypi
mistune 2.0.5 pypi_0 pypi
msgpack 1.0.5 pypi_0 pypi
mypy-extensions 1.0.0 pypi_0 pypi
ncurses 6.4 hcb278e6_0 conda-forge
networkx 3.1 pypi_0 pypi
numpy 1.25.0 pypi_0 pypi
openssl 3.1.1 hd590300_1 conda-forge
packaging 23.1 pypi_0 pypi
pandas 2.0.3 pypi_0 pypi
patsy 0.5.3 pypi_0 pypi
pillow 10.0.0 pypi_0 pypi
pip 23.1.2 pyhd8ed1ab_0 conda-forge
prov 1.5.1 pypi_0 pypi
psutil 5.9.5 pypi_0 pypi
pydot 1.4.2 pypi_0 pypi
pyparsing 3.1.0 pypi_0 pypi
python 3.11.4 hab00c5b_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
pytz 2023.3 pypi_0 pypi
rdflib 6.3.2 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pypi_0 pypi
ruamel-yaml 0.17.32 pypi_0 pypi
ruamel-yaml-clib 0.2.7 pypi_0 pypi
schema-salad 8.4.20230606143604 pypi_0 pypi
scipy 1.11.1 pypi_0 pypi
seaborn 0.12.2 pypi_0 pypi
setuptools 68.0.0 pyhd8ed1ab_0 conda-forge
shellescape 3.8.1 pypi_0 pypi
six 1.16.0 pypi_0 pypi
statsmodels 0.14.0 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
typing-extensions 4.7.1 pypi_0 pypi
tzdata 2023.3 pypi_0 pypi
urllib3 2.0.3 pypi_0 pypi
websocket-client 1.6.1 pypi_0 pypi
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
I get this error code:
NFO [workflow ] start
INFO [workflow ] starting step fastp_pe
INFO [step fastp_pe] start
INFO ['singularity', 'pull', '--force', '--name', 'quay.io_biocontainers_fastp:0.20.0--hdbcaa40_0.sif', 'docker://quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0']
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0: not a valid image manifest or image index
ERROR Workflow or tool uses unsupported feature:
Singularity is required to run this tool: Command '['singularity', 'pull', '--force', '--name', 'quay.io_biocontainers_fastp:0.20.0--hdbcaa40_0.sif', 'docker://quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0']' returned non-zero exit status 255.
Do you understand this error message or what could be wrong here? I do not use Singularity for anything but your package so I do not understand it very well. Thank you for your time.
Hmm, sorry, I can't understand what is the optimal solution for this.
Could you ask it in cwltools repo if the issue still exists?
https://github.com/common-workflow-language/cwltool