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CVUA-RRW / FooDMe

A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
https://cvua-rrw.github.io/FooDMe
BSD 3-Clause "New" or "Revised" License
4 stars 1 forks source link

Foodme environment error #44

Closed gregdenay closed 2 years ago

gregdenay commented 2 years ago

Under Debian 11

Job 1: Generating global html report

Activating conda environment: .snakemake/conda/49331715801f124dd0f1cdc91c25109a
ERROR: This cross-compiler package contains no program /home/warmann/foodme/FooDMe/.snakemake/conda/49331715801f124dd0f1cdc91c25109a/bin/x86_64-conda_cos6-linux-gnu-gfortran
INFO: activate-gfortran_linux-64.sh made the following environmental changes:
+HOST=x86_64-conda_cos6-linux-gnu
-HOST=x86_64-conda-linux-gnu
[Fri May  6 10:33:09 2022]
Finished job 1.
27 of 28 steps (96%) done
Select jobs to execute...

[Fri May  6 10:33:09 2022]
localrule all:
    input: reports/report.html
    jobid: 0
    resources: tmpdir=/tmp

[Fri May  6 10:33:09 2022]
Finished job 0.
28 of 28 steps (100%) done
Complete log: .snakemake/log/2022-05-06T102756.305089.snakemake.log

Workflow finished, no error

Workflow finishes without errors BUT .html is not produced

gregdenay commented 2 years ago

snakemake --use-conda --conda-prefix ~/2022-05-06_foodme_test/ --cores 1 --conda-create-envs-only --forceall

(base) warmann@BS-B-NGS-Main:~/foodme/FooDMe$ conda activate foodme
ERROR: This cross-compiler package contains no program /home/warmann/miniconda3/envs/foodme/bin/x86_64-conda_cos6-linux-gnu-c++
ERROR: activate-gxx_linux-64.sh failed, see above for details
(foodme) warmann@BS-B-NGS-Main:~/foodme/FooDMe$ snakemake --use-conda --conda-prefix ~/2022-05-06_foodme_test/ --cores 1 --conda-create-envs-only --forceall
Building DAG of jobs...
Creating conda environment ../workflow/envs/blast.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/blast.yaml created (location: ../../../2022-05-06_foodme_test/4df931caa189e5be269550225f4a90b6)
Creating conda environment ../workflow/envs/taxidtools.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/taxidtools.yaml created (location: ../../../2022-05-06_foodme_test/9ee622447d1fa2c35b98d9897a56a359)
Creating conda environment ../workflow/envs/rmarkdown.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/rmarkdown.yaml created (location: ../../../2022-05-06_foodme_test/34e4f0d7e9a3b16493b7df839a70b367)
Creating conda environment ../workflow/envs/seqtk.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/seqtk.yaml created (location: ../../../2022-05-06_foodme_test/5fc4d10a7749193d30fa55e6d720f737)
Creating conda environment ../workflow/envs/fastp.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/fastp.yaml created (location: ../../../2022-05-06_foodme_test/62b46e620846c0c130106d17a127fa90)
Creating conda environment ../workflow/envs/cutadapt.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/cutadapt.yaml created (location: ../../../2022-05-06_foodme_test/e7d2c0a956e732849b6803eb2b448dfc)
Creating conda environment ../workflow/envs/krona.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/krona.yaml created (location: ../../../2022-05-06_foodme_test/0a838b3aec865e86b7539a1e6dbdbc38)
Creating conda environment ../workflow/envs/pandas.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/pandas.yaml created (location: ../../../2022-05-06_foodme_test/f9e36becbc7441e42e39424159e84d43)
Creating conda environment ../workflow/envs/dada2.yaml...
Downloading and installing remote packages.
Environment for /home/warmann/foodme/FooDMe/workflow/rules/../envs/dada2.yaml created (location: ../../../2022-05-06_foodme_test/dfd0b17fbc8d82568108a604ec5d31ba)

The problem is in the base environment

gregdenay commented 2 years ago

Possibly related to https://github.com/conda/conda/issues/6600

gregdenay commented 2 years ago

Error can not be reproduced on Debian10 or Ubuntu 20-4 Most likely an error in the creation of the base environment.