Troubleshooting¶

How do I report ElasticBLAST problems?¶

Please see Support.

How do I see resources created by ElasticBLAST?¶

If you are running ElasticBLAST on GCP:

Please check the GCP web console or run the commands below:

gcloud container clusters list
gcloud compute disks list

If you are running ElasticBLAST on AWS:

Please check the AWS web console or run the commands below:

aws cloudformation describe-stacks --stack-name elasticblast-${USER} --output text
aws ec2 describe-instances --filter Name=tag:billingcode,Values=elastic-blast Name=tag:Owner,Values=${USER} --query "Reservations[*].Instances[*].InstanceId" --output text

My search seems to be stalled¶

Run the commands below to see what is running in your GCP GKE cluster:

kubectl logs -l app=setup --timestamps
kubectl logs -l app=blast -c blast --timestamps
kubectl logs -l app=blast -c results-export --timestamps
kubectl get pods -o name -l app=blast | sed 's,pod/,,' | xargs -t -I{} kubectl exec {} -c blast -- top -n1 -cb
kubectl get pods -o name -l app=blast | sed 's,pod/,,' | xargs -t -I{} kubectl exec {} -c blast -- ps aux

If you want to stop the search, run the command below to delete all cloud resources created by ElasticBLAST. Your input file(s) will not be modified.

./elastic-blast delete --cfg ${CONFIG_FILE} --loglevel DEBUG

I cannot find python or an expected version when I run elastic-blast¶

Run

python --version

to see which version of python you have (or if it’s even installed). If python is not found or it is not one of the supported versions (3.6, 3.7 or 3.8), you will need to install it (3.8 recommended). If one of versions from 3.6, 3.7 or 3.8 is found, then you can try the corresponding elastic-blast script (e.g., elastic-blast3.8).

I get a message about not being able write into the bucket with submit command¶

Things to check:

You are logged in with the correct account (e.g., your institutional GCP account and not your personal gmail account). Check this with:

gcloud config get-value account

The bucket URI (in the “results-bucket” field of the config file) starts with gs://. For example, the bucket URI should be gs://sarahtest but instead you have “sarahtest”.
The bucket URI is correct and you have permission to write to it. The GCP page on bucket permissions is at https://cloud.google.com/storage/docs/gsutil/commands/acl but it is probably easiest to try and copy a file into your bucket with:

date > date.txt
gsutil cp date.txt ${YOUR_RESULTS_BUCKET}

I get a message about a project not existing¶