samnooij
commented
1 month ago Please refer to the original repository at https://gitlab.lcsb.uni.lu/laura.denies/PathoFact This repository is a fork and little personal hobby project that is not supported and no longer maintained. Sorry!
Hi, I have problems running the test files. Everytime I run it, have this error:
[Thu Aug 8 15:58:49 2024] Job 42: Execute classifier for virulence factor prediction on the following sample(s): output_test - test_sample Reason: Missing output files: test/output_test/PathoFact_intermediate/VIRULENCE/classifier_virulence/test_sample/group_1_classifier_prediction.tsv; Input files updated by another job: test/output_test/PathoFact_intermediate/VIRULENCE/classifier_virulence/test_sample/group_1_matrix.tsv
python scripts/virulence_prediction.py test/output_test/PathoFact_intermediate/VIRULENCE/classifier_virulence/test_sample/group_1_matrix.tsv test/output_test/PathoFact_intermediate/VIRULENCE/classifier_virulence/test_sample/group_1_classifier_prediction.tsv scripts/Virulence_factor_model.sav &> test/output_test/logs/test_sample/group_1_classifier_prediction.log Activating conda environment: /home/champa/PathoFact/.snakemake/conda/1f0c605d Activating conda environment: /home/champa/PathoFact/.snakemake/conda/7da68472 Activating conda environment: /home/champa/PathoFact/.snakemake/conda/7da68472 Updating job 22. Updating job 23. Creating conda environment envs/rgi.yaml... Downloading remote packages. Environment for envs/rgi.yaml created (location: .snakemake/conda/9dc4e991) Creating conda environment envs/DeepARG.yaml... Downloading remote packages. [Thu Aug 8 15:59:21 2024] Error in rule splitting: jobid: 31 output: test/output_test/PathoFact_intermediate/splitted/test_sample/ log: test/output_test/PathoFact_intermediate/logs/test_sample/split_ORF.log (check log file(s) for error message) conda-env: /home/champa/PathoFact/.snakemake/conda/7da68472 shell:
[Thu Aug 8 15:59:21 2024] Finished job 3. 5 of 25 steps (20%) done Removing temporary output file test/output_test/PathoFact_intermediate/VIRULENCE/classifier_virulence/test_sample/group_1_matrix.tsv. [Thu Aug 8 15:59:21 2024] Finished job 42. 6 of 25 steps (24%) done Removing output files of failed job splitting since they might be corrupted: test/output_test/PathoFact_intermediate/splitted/test_sample/ Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/champa/PathoFact/.snakemake/log/2024-08-08T155848.735372.snakemake.log
split_ORF.log
This is the command I use : snakemake -s test/Snakefile --use-conda --reason --cores -p -w 30
I checked all dependencies and they do not seem to be the problem. Can you help me please, I have been on that for at least a week and I don't know what to do anymore.
Thank you :)