Hi, we are trying to release #C01U1E95JQ5 https://github.com/nf-core/magmap/pull/191 but we are having issue with nf-tests that uses Conda. in particular, it seems to fail when trying to run Prokka (which it seems to not have parallel, see below). Do you have any idea of how to fix that? Thanks!

> ERROR ~ Error executing process > 'NFCORE_MAGMAP:MAGMAP:PROKKA (GCF_001983105.1)'
    >
    > Caused by:
    >   Process `NFCORE_MAGMAP:MAGMAP:PROKKA (GCF_001983105.1)` terminated with an error exit status (2)
    >
    >
    > Command executed:
    >
    >   gunzip -c GCF_001983105.1_ASM198310v1_genomic.fna.gz > GCF_001983105.1_ASM198310v1_genomic.fna
    >
    >   prokka \
    >       --centre X --compliant \
    >       --cpus 2 \
    >       --prefix GCF_001983105.1 \
    >        \
    >        \
    >       GCF_001983105.1_ASM198310v1_genomic.fna
    >
    >   rm GCF_001983105.1_ASM198310v1_genomic.fna
    >
    >   gzip GCF_001983105.1/*
    >
    >   cat <<-END_VERSIONS > versions.yml
    >   "NFCORE_MAGMAP:MAGMAP:PROKKA":
    >       prokka: $(echo $(prokka --version 2>&1) | sed 's/^.*prokka //')
    >   END_VERSIONS
    >
    > Command exit status:
    >   2
    >
    > Command output:
    >   (empty)
......

>   [06:55:58] Running: cat GCF_001983105\.1\/GCF_001983105\.1\.IS\.tmp\.20249\.faa | parallel --gnu --plain -j 2 --block 667437 --recstart '>' --pipe blastp -query - -db /home/runner/_work/magmap/magmap/~/tests/adc2f77fc05b775a45a6437e4efc7ee5/work/conda/env-032f4f71e2f3f76834e40cf9b2ecf6e2/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > GCF_001983105\.1\/GCF_001983105\.1\.IS\.tmp\.20249\.blast 2> /dev/null
    >   [06:55:58] Could not run command: cat GCF_001983105\.1\/GCF_001983105\.1\.IS\.tmp\.20249\.faa | parallel --gnu --plain -j 2 --block 667437 --recstart '>' --pipe blastp -query - -db /home/runner/_work/magmap/magmap/~/tests/adc2f77fc05b775a45a6437e4efc7ee5/work/conda/env-032f4f71e2f3f76834e40cf9b2ecf6e2/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > GCF_001983105\.1\/GCF_001983105\.1\.IS\.tmp\.20249\.blast 2> /dev/null

I see that the bioconda package has parallel >=20180522 (linux-64/prokka-1.12-pl526_0.tar.bz2)

I see, then would it be easier to just change

NFT_WORKDIR: ${{ runner.temp }}

in the

nf-test.yml

?

agree!

I will give it a try, many thanks!

can you try following this? https://github.com/nf-core/rnaseq/blob/master/.github/workflows/nf-test.yml

I did it but with the same results. the error seems to be with

prokka

and I think rnaseq doesn't use it in the pipeline. So probably the didn't have to deal with this error.

looking at here: https://github.com/nf-core/magmap/actions/runs/26515069201/job/78089919783?pr=191 I think this may be relevant: https://github.com/tseemann/prokka/issues/564

That's an useful information. Most likely we will not fix the bug by our own. <!subteam^S016E36N7TQ> We can't run conda nf-tests on the release PR of #C01U1E95JQ5 since there is a bug in Prokka tool itself (look at the last message from @piplus2). Is it fine if we go ahead and merge the release PR even without having the nf-tests for conda passed? (all the tests with Singularity, Docker and the full tests passed).

You could have a conda ignore list

Did you try with a previous version of

prokka

? I don't know if it's a bug introduced in the latest updates. Maybe that would fix... otherwise as @Maxime Garcia wrote

You need to include the no_conda in your ci as well. We can talk about it tomorrow if you want. Sarek CI is a bit wild 😂

yep, I was looking now at

UTILS.groovy

too, I guess it's related.

I should explain that whole idea one day

Interesting @Danilo Di Leo before you do that maybe search in #CE9MS66BS we've definitely seen that error before

No tests issues if you don't run the tests

I see something here that may be related https://github.com/nf-core/modules/pull/11754 @Joon Klaps?

shared a GIF

it seems that @Joon Klaps fixed that problem here https://github.com/nf-core/modules/issues/11517. maybe he can help you

Yeah was facing the same issues in #C0905QCFTPE, saw the initial issue description in https://github.com/nf-core/modules/issues/11517 hence the PR https://github.com/nf-core/modules/pull/11754. If you pull latest version of prokka from nf-core modules, that should resolve it. Else there is another bug we missed.

Hello, thanks you all for the help! I just did the update of

prokka

and re-run the test in the PR release. I ended up with another error:

> ERROR ~ Error executing process > 'NFCORE_MAGMAP:MAGMAP:PROKKA (1)'
    >
    > Caused by:
    >   Failed to create Conda environment
    >     command: conda env create --prefix /home/runner/_work/magmap/magmap/~/tests/6e7e5413c69b417fae98a4dc1fb122fd/work/conda/env-8a6013d25d6b85ab556468d8f4e59d30 --file /home/runner/_work/magmap/magmap/modules/nf-core/prokka/environment.yml
    >     status : 1
    >     message:
    >       CI detected...
    >       Channels:
    >        - conda-forge
    >        - bioconda
    >       Platform: linux-64
    >       Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ failed
    >
    >       # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
    >
    >           Traceback (most recent call last):
    >             File "/usr/share/miniconda/lib/python3.13/site-packages/conda/exception_handler.py", line 30, in __call__
    >               return func(*args, **kwargs)
    >             File "/usr/share/miniconda/lib/python3.13/site-packages/conda/cli/main.py", line 62, in main_subshell
    >               exit_code = do_call(args, parser)
    >             File "/usr/share/miniconda/lib/python3.13/site-packages/conda/cli/conda_argparse.py", line 189, in do_call
    >               result = getattr(module, func_name)(args, parser)
    >                                 x_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin
    >                                 :/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/
    >                                 usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/bi
    >                                 n/
    >                 PKG_CONFIG_PATH=/opt/hostedtoolcache/Python/3.14.5/x64/lib/pkgconfig
    >                Python2_ROOT_DIR=/opt/hostedtoolcache/Python/3.14.5/x64
    >                Python3_ROOT_DIR=/opt/hostedtoolcache/Python/3.14.5/x64
    >                 Python_ROOT_DIR=/opt/hostedtoolcache/Python/3.14.5/x64
    >              REQUESTS_CA_BUNDLE=<not set>
    >               SELENIUM_JAR_PATH=/usr/share/java/selenium-server.jar
    >                   SSL_CERT_FILE=<not set>
    >                  pythonLocation=/opt/hostedtoolcache/Python/3.14.5/x64
    >
    >            active environment : None
    >              user config file : /home/runner/.condarc
    >        populated config files : /usr/share/miniconda/.condarc
    >                                 /usr/share/miniconda/condarc.d/anaconda-auth.yml
    >                                 /home/runner/.condarc
    >                 conda version : 26.3.2
    >           conda-build version : not installed
    >                python version : 3.13.13.final.0
    >                        solver : libmamba (default)
    >              virtual packages : __archspec=1=sapphirerapids
    >                                 __conda=26.3.2=0
    >                                 __glibc=2.39=0
    >                                 __linux=6.17.0=0
    >                                 __unix=0=0
    >              base environment : /usr/share/miniconda  (writable)
    >             conda av data dir : /usr/share/miniconda/etc/conda
    >         conda av metadata url : None
    >                  channel URLs : <https://conda.anaconda.org/conda-forge/linux-64>
    >                                 <https://conda.anaconda.org/conda-forge/noarch>
    >                                 <https://conda.anaconda.org/bioconda/linux-64>
    >                                 <https://conda.anaconda.org/bioconda/noarch>
    >                 package cache : /home/runner/conda_pkgs_dir
    >              envs directories : /usr/share/miniconda/envs
    >                                 /home/runner/.conda/envs
    >           temporary directory : /tmp
    >                      platform : linux-64
    >                    user-agent : conda/26.3.2 requests/2.33.1 CPython/3.13.13 Linux/6.17.0-1015-aws ubuntu/24.04.4 glibc/2.39 solver/libmamba conda-libmamba-solver/26.4.0 libmambapy/2.3.2 aau/0.7.6 c/. s/. e/.
    >                       UID:GID : 1001:1001
    >                    netrc file : None
    >                  offline mode : False
    >
    >
    >       An unexpected error has occurred. Conda has prepared the above report.
    >       If you suspect this error is being caused by a malfunctioning plugin,
    >       consider using the --no-plugins option to turn off plugins.
    >
    >       Example: conda --no-plugins install <package>
    >
    >       Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
    >       the command line to run the command without plugins enabled.
    >
    >       Example: CONDA_NO_PLUGINS=true conda install <package>

So something is still not working in the creation of the conda environment. Since we have a bit of rush with the release of the pipeline, I would go with the suggestion of @Maxime Garcia and as soon the bug it's fixed, I will update the module and remove the

no_conda

option.

you may want to look at this error

sqlite3.OperationalError: database is locked

it happened when creating the conda env for prokka.