Troubleshooting¶

View the log file¶

If you submitted the pipeline to slurm, there will be a slurm log file log/ with the name log/slurm_${SLURM_JOB_ID}.log. Otherwise, it will be printed to standard output and standard error in your terminal.

Try resubmitting¶

If you are running the pipeline on a cluster, try resubmitting the job. Sometimes jobs fail due to temporary issues with the cluster or resources.

CHAMPAGNE uses -resume by default, so calling champagne run with the same options as your original run will resume the pipeline from where it left off, rather than starting over. If you do want to start over, use --forceall with champagne run.

Getting Help¶

If you think your issue is a bug, open an issue and include a minimal reproducible example.

If you have a general question about the pipeline, ask it in discussions.

General Inquiries and Collaboration: Please contact the CCBR Pipeliner team at CCBR_Pipeliner@mail.nih.gov.