I’m trying to use the annotation database with the example 1kg VDS file, but keep getting errors like the below:
Job [c0475ca9-27ad-4e1a-833e-622e8ddeceef] submitted. Waiting for job output... Running on Apache Spark version 2.0.2 SparkUI available at http://10.132.0.2:4040 Welcome to __ __ <>__ / /_/ /__ __/ / / __ / _ `/ / / /_/ /_/\_,_/_/_/ version 0.1-0d9e264 2017-09-08 22:45:54 Hail: WARN: called redundant split on an already split VDS Traceback (most recent call last): File "/tmp/c0475ca9-27ad-4e1a-833e-622e8ddeceef/annot.py", line 10, in <module> 'va.gencode19' File "/home/ec2-user/BuildAgent/work/4d93753832b3428a/python/hail/dataset.py", line 997, in annotate_variants_db sqlite3.OperationalError: too many terms in compound SELECT ERROR: (gcloud.dataproc.jobs.submit.pyspark) Job [c0475ca9-27ad-4e1a-833e-622e8ddeceef] entered state [ERROR] while waiting for [DONE].
I’ve tried with both this file as well as a sites only VDS generated from a fairly generic variant list. any advice much appreciated.