yyoshiaki
commented
1 month ago 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
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.