Trouble with VEP GRCh37

Hail Query & hailctl
1

For the past few days, i am getting an error message whenever i try to initiate the cluster with --vep GRCh37.

I am getting the following error message:

Initialization action failed. Failed action ‘gs://hail-common/hailctl/dataproc/0.2.23/vep-GRCh37.sh’, see output in: gs://wes_development/google-cloud-dataproc-metainfo/b93872f2-a05e-4fe3-a6ac-3879d9448028/hailjupy-m/dataproc-initialization-script-1_output

When i look at the output file, i get the following message in the last lines:

Status: Downloaded newer image for konradjk/vep85_loftee:1.0.3
docker.io/konradjk/vep85_loftee:1.0.3
CommandException: No URLs matched: gs://hail-common/vep/vep/loftee-beta/GRCh37/1var.vcf
cat: /1var.vcf: No such file or directory
ERROR: No cache found for homo_sapiens, version 85

I get no error messages when i initiate with --VEP GRCh38.

I would be thankful for your help.

Thanks

Danish

2

I have updated hail which resolved the above problem. However, I am now having a new problem.

failed: Initialization action failed. Failed action ‘gs://hail-common/hailctl/dataproc/0.2.46/init_notebook.py’, see output in: gs://wes_development/google-cloud-dataproc-metainfo/3427c8dd-67a7-466f-bbb9-38f22adeff25/hailjupy-m/dataproc-initialization-script-0_output.

In the output, i see the following last lines

Traceback (most recent call last):
File “/etc/google-dataproc/startup-scripts/dataproc-initialization-script-0”, line 64, in
safe_call(*command)
File “/etc/google-dataproc/startup-scripts/dataproc-initialization-script-0”, line 18, in safe_call
print(e.output).decode()
AttributeError: ‘NoneType’ object has no attribute ‘decode’

3

Kindly help

4

See solution at Problem of running VEP on HAIL