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Problem loading SNPeff annotated VCF #1390
Trying to load a SNPEff annotated VCF into ADAM 0.21.0 using Scala 2.10. Tried loading of VCFs in ADAM 0.19.0 and this works (also using Kryo-2.24). Getting the Kryo exception below:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 4 times, most recent failure: Lost task 0.3 in stage 0.0 (TID 6, spiro.intec.ugent.be): java.io.EOFException
Hi @ddemaeyer! Sorry for the slow reply, a few of us have been out-of-the-office sporadically this week. Which version of Spark are you running, and how are you deploying Spark (e.g., in Mesos, on YARN, etc). Is this the only error you are seeing? Sometimes serialization will fail and there will be two errors thrown: one where the serializer failed, and one where the deserialization failed (that would be this error message).