Closed olgabot closed 5 years ago
The crash is a bug. That said, I think your cache (assoc) configuration is not working. This crash occurs because the assoc is nil. Can you make sure your dynamodb exists and your config has an assoc field that has the correct dynamodb table name?
Thanks, yes I was able to fix it by adding the fields to our config. Since not everyone has permission to create tables in our AWS account, we simply concatenate the fields to the config.yaml file:
# Add czbiohub caches to the config
REFLOW_CONFIG=$HOME/.reflow/config.yaml
echo 'repository: s3,czbiohub-reflow-quickstart-cache' >> $REFLOW_CONFIG
echo 'assoc: dynamodb,czbiohub-reflow-quickstart' >> $REFLOW_CONFIG
Not sure what is happening here but getting this error here. As a side note, there were 5 jobs for
star.Index
running simultaneously when really there only should be ONE job since the same genome is getting used by all the runsHere's the command and error:
Here are the samples.csv and config.json, where
rnaseq.rf
is this workflow.Here's a screenshot of the final output, showing that the existing instances haven't been shut down properly after the
reflow runbatch
failed.