Evapatrick
commented
4 months ago managed to resolve the issue by using : conda config --set channel_priority disabled
Closed Evapatrick closed 4 months ago
Evapatrick
commented
4 months ago managed to resolve the issue by using : conda config --set channel_priority disabled
Hi I am encountering the issue below when trying to run my own data. please help (phables) bsl@bsl-ubuntu:~/phables.out/phables.out$ phables run --input /home/bsl/Downloads/assembly_graph_with_scaffolds.gfa --reads /home/bsl/Downloads/CS-002/ --threads 8 [2024:02:22 16:27:51] Copying system default config to phables.out/config.yaml [2024:02:22 16:27:51] Updating config file with new values [2024:02:22 16:27:51] Writing config file to phables.out/config.yaml [2024:02:22 16:27:51] ------------------ [2024:02:22 16:27:51] | Runtime config | [2024:02:22 16:27:51] ------------------
alpha: 1.2 compcount: 200 conda_prefix: /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/conda configfile: phables.out/config.yaml covtol: 100 databases: null evalue: 1.0e-10 input: /home/bsl/Downloads/assembly_graph_with_scaffolds.gfa log: phables.out/phables.log longreads: false maxpaths: 10 mgfrac: 0.2 mincov: 10 minlength: 2000 output: phables.out profile: null reads: /home/bsl/Downloads/CS-002/ resources: jobCPU: 8 jobMem: 16000 seqidentity: 0.3 snake_args: [] snake_default:
[2024:02:22 16:27:51] --------------------- [2024:02:22 16:27:51] | Snakemake command | [2024:02:22 16:27:51] ---------------------
snakemake -s /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/phables.smk --configfile phables.out/config.yaml --cores 8 --use-conda --conda-prefix /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/conda --rerun-incomplete --printshellcmds --nolock --show-failed-logs Restricted license - for non-production use only - expires 2025-11-24 Config file /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/../config/config.yaml is extended by additional config specified via the command line. Config file /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/../config/databases.yaml is extended by additional config specified via the command line. Output files will be saved to directory, phables.out
Assuming unrestricted shared filesystem usage for local execution. Building DAG of jobs... Creating conda environment /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/rules/../envs/smg.yaml... Downloading and installing remote packages. Environment for /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/rules/../envs/smg.yaml created (location: ../../micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/0d6d2a505e3fcf3ed3a28fc804e186f6) Creating conda environment /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/rules/../envs/koverage.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/rules/../envs/koverage.yaml: Command: mamba env create --quiet --file "/home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/9b971e1782ecf56623a7caa7bcc0da6b.yaml" --prefix "/home/bsl/micromamba/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/9b971e1782ecf56623a7caa7bcc0da6b_" Output: warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY Could not solve for environment specs The following package could not be installed └─ koverage >=0.1.6 is uninstallable because it requires └─ datapane >=0.16.7 but there are no viable options ├─ datapane 0.16.7 would require │ └─ boltons >=20.0.0,<22.0.0 , which conflicts with any installable versions previously reported; └─ datapane 0.17.0 would require └─ dominate >=2.7.0,<3.0.0 , which conflicts with any installable versions previously reported.
[2024:02:22 16:28:44] ERROR: Snakemake failed