AssertionError exception

Hail Query & hailctl
1

I have another exception. In this case is not loading, is after that, when I try to export genotypes. Count is ok so I suppose is related with genotypes format.

020-09-19 09:51:39 DAGScheduler: INFO: ResultStage 14 (runJob at ContextRDD.scala:228) failed in 253.579 s due to Job aborted due to stage failure: Task 759 in stage 14.0 failed 1 times, most recent failure: Lost task 759.0 in stage 14.0 (TID 8994, localhost, executor driver): java.lang.AssertionError: assertion failed
at scala.Predef$.assert(Predef.scala:156)
at is.hail.io.vcf.VCFLine.nextField(LoadVCF.scala:298)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1448)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1302)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1739)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1732)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$18.hasNext(Iterator.scala:759)
at scala.collection.Iterator$$anon$16.hasNext(Iterator.scala:598)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
at is.hail.annotations.OrderedRVIterator$$anon$1.next(OrderedRVIterator.scala:200)
at is.hail.annotations.OrderedRVIterator$$anon$1.next(OrderedRVIterator.scala:180)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:445)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:410)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:463)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1222)
at is.hail.rvd.RVD$$anonfun$32.apply(RVD.scala:1221)
at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:232)
at is.hail.sparkextras.ContextRDD$$anonfun$crunJobWithIndex$1.apply(ContextRDD.scala:230)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)

2

So we should throw a better error message here, but it looks like that happens because there wasn’t a tab character present in between two of the sample fields.

3

Looks like this is called to parse the tab delimiter between chrom/pos/rsid/ref/alts, and one of those is missing a tab

4

definitely should throw an error about malformatted file instead of an assertion

5