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Hi Matin,
when I run bgcflow build report on the Lactobacillus_delbrueckii example dataset, I get this error for the generation of the eggNOG-Roary markdown:
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-26T090317.499563.snakemake.log WorkflowError: At least one job did not complete successfully.
I examined the log file (attached) and I noticed a problem in executing the Rare pangene category cell:
I thought it's because rare pangenes are not classified in the Lactobacillus_delbrueckii example dataset, so the cell can't be run for the generation of the markdown.
Indeed, I erased that cell and I managed to generate and serve that report.
I think you should include a rule to skip cells if pangenes for those categories haven't been classified, so that reports can be built and served correctly with the information available,
The text was updated successfully, but these errors were encountered:
Thanks for the feedback and suggestion! Will follow up on this.
andrekind17
changed the title
Error in Generating Markdown Report for eggNOG - Proposed Solution
Error in Generating Markdown Report for eggNOG-Roary - Proposed Solution
Sep 26, 2024
Hi Matin,
when I run
bgcflow build report
on the Lactobacillus_delbrueckii example dataset, I get this error for the generation of the eggNOG-Roary markdown:Error in rule mkdocs_py_report: jobid: 31 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/eggnog-roary.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/eggnog-roary.md log: logs/report/eggnog-roary-report-Lactobacillus_delbrueckii.log (check log file(s) for error details) conda-env: /mnt/data/studenti/agentile/bgcflow/.snakemake/conda/e9d7fcc98b88235172f4b2a161bfc170_ shell:
jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/eggnog-roary.ipynb --no-input --output eggnog-roary.md 2>> logs/report/eggnog-roary-report-Lactobacillus_delbrueckii.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-26T090317.499563.snakemake.log WorkflowError: At least one job did not complete successfully.
I examined the log file (attached) and I noticed a problem in executing the Rare pangene category cell:
KeyError: 'Rare'
eggnog-roary-report-Lactobacillus_delbrueckii.log
I thought it's because rare pangenes are not classified in the Lactobacillus_delbrueckii example dataset, so the cell can't be run for the generation of the markdown.
Indeed, I erased that cell and I managed to generate and serve that report.
I think you should include a rule to skip cells if pangenes for those categories haven't been classified, so that reports can be built and served correctly with the information available,
The text was updated successfully, but these errors were encountered: