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Missing key error #4799

konradjk opened this issue Nov 18, 2018 · 2 comments


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commented Nov 18, 2018

I wonder if related to #4754?

ht = hl.experimental.import_gtf('gs://konradk/gencode.v19.annotation.gtf.bgz', 'GRCh37', True, min_partitions=12)
ht = ht.annotate(gene_id=ht.gene_id.split('\\.')[0],
                 length=ht.interval.end.position - ht.interval.start.position + 1)
coding_regions = ht.filter(ht.feature == 'CDS').select('gene_id', 'transcript_id', 'transcript_type', 'length', 'level')
transcripts = coding_regions.group_by('transcript_id', 'transcript_type', 'gene_id',


transcripts.count()  # fails with error below
transcripts.persist().count() # succeeds

on current master (d33e2d1)

Py4JJavaError: An error occurred while calling
: java.util.NoSuchElementException: key not found: interval
	at scala.collection.MapLike$class.default(MapLike.scala:228)
	at scala.collection.AbstractMap.default(Map.scala:59)
	at scala.collection.MapLike$class.apply(MapLike.scala:141)
	at scala.collection.AbstractMap.apply(Map.scala:59)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
	at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
	at scala.collection.TraversableLike$
	at is.hail.rvd.RVDType.<init>(RVDType.scala:23)
	at is.hail.expr.types.TableType.<init>(TableType.scala:16)
	at is.hail.expr.types.TableType.copy(TableType.scala:15)
	at scala.PartialFunction$Lifted.apply(PartialFunction.scala:223)
	at scala.PartialFunction$Lifted.apply(PartialFunction.scala:219)

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commented Nov 19, 2018

Just got something like this on a completely separate pipeline. This appears to occur after grouping on something and not including a previous key. FWIW works with a4f79a3

cc @jbloom22


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commented Dec 6, 2018

Ok confirmed this was not fixed by #4867 - any ideas?

@tpoterba tpoterba self-assigned this Dec 6, 2018

tpoterba added a commit to tpoterba/hail that referenced this issue Dec 6, 2018

tpoterba added a commit to tpoterba/hail that referenced this issue Dec 6, 2018

@danking danking closed this in #4904 Dec 6, 2018

danking added a commit that referenced this issue Dec 6, 2018

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