inred created SPARK-18263:
-----------------------------
Summary: configures the serializer programatically failed
Key: SPARK-18263
URL: https://issues.apache.org/jira/browse/SPARK-18263
Project: Spark
Issue Type: Bug
Components: Spark Core
Affects Versions: 2.0.1
Environment: spark-2.0.1-bin-hadoop2.6
scala-2.11.8
Reporter: inred
spark.conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
spark.conf.set("spark.kryo.registrator",
"org.bdgenomics.adam.serialization.ADAMKryoRegistrator")
it reports the following error:
java.io.NotSerializableException: org.bdgenomics.formats.avro.AlignmentRecord
Serialization stack:
object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord,
value: {"readInFragment": 0, "contigName": "chr10", "start": 61758687,
"oldPosition": null, "end": 61758727, "mapq": 25, "readName":
"NB501244AR:119:HJY3WBGXY:2:11112:6137:19359", "sequence":
"AAAATACTGAGACTTATCAGAATTTCAGGCTAAAGCAACC", "qual":
"AAAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null,
"basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false,
"properPair": false, "readMapped": true, "mateMapped": false,
"failedVendorQualityChecks": false, "duplicateRead": false,
"readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment":
true, "secondaryAlignment": false, "supplementaryAlignment": false,
"mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName":
null, "recordGroupSample": null, "mateAlignmentStart": null,
"mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize": null})
at
org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:40)
at
org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:46)
at
org.apache.spark.serializer.SerializationStream.writeValue(Serializer.scala:135)
at
org.apache.spark.storage.DiskBlockObjectWriter.write(DiskBlockObjectWriter.scala:185)
at
org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:150)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 0.0 in stage 2.0 (TID 9) had
a not serializable result: org.bdgenomics.formats.avro.AlignmentRecord
Serialization stack:
object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord,
value: {"readInFragment": 0, "contigName": "chr1", "start": 10001,
"oldPosition": null, "end": 10041, "mapq": 0, "readName":
"NB501244AR:119:HJY3WBGXY:3:11508:7857:8792", "sequence":
"AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC", "qual":
"///E////6E////EEAEEE/EEEEEEEEEEEEAEAAA/A", "cigar": "40M", "oldCigar": null,
"basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false,
"properPair": false, "readMapped": true, "mateMapped": false,
"failedVendorQualityChecks": false, "duplicateRead": false,
"readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment":
true, "secondaryAlignment": false, "supplementaryAlignment": false,
"mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:R\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX0:i:594", "recordGroupName": null,
"recordGroupSample": null, "mateAlignmentStart": null, "mateAlignmentEnd":
null, "mateContigName": null, "inferredInsertSize": null}); not retrying
2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 4.0 in stage 2.0 (TID 13)
had a not serializable result: org.bdgenomics.formats.avro.AlignmentRecord
Serialization stack:
object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord,
value: {"readInFragment": 0, "contigName": "chr10", "start": 61758687,
"oldPosition": null, "end": 61758727, "mapq": 25, "readName":
"NB501244AR:119:HJY3WBGXY:2:11112:6137:19359", "sequence":
"AAAATACTGAGACTTATCAGAATTTCAGGCTAAAGCAACC", "qual":
"AAAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null,
"basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false,
"properPair": false, "readMapped": true, "mateMapped": false,
"failedVendorQualityChecks": false, "duplicateRead": false,
"readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment":
true, "secondaryAlignment": false, "supplementaryAlignment": false,
"mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName":
null, "recordGroupSample": null, "mateAlignmentStart": null,
"mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize": null});
not retrying
2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 3.0 in stage 2.0 (TID 12)
had a not serializable result: org.bdgenomics.formats.avro.AlignmentRecord
Serialization stack:
object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord,
value: {"readInFragment": 0, "contigName": "chr7", "start": 68163823,
"oldPosition": null, "end": 68163863, "mapq": 0, "readName":
"NB501244AR:119:HJY3WBGXY:4:21602:16293:18064", "sequence":
"TGTGAGGGTGTTGCCCAAAAGAGATTAACATTTGAGTCAG", "qual":
"AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null,
"basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false,
"properPair": false, "readMapped": true, "mateMapped": false,
"failedVendorQualityChecks": false, "duplicateRead": false,
"readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment":
true, "secondaryAlignment": false, "supplementaryAlignment": false,
"mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:R\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tXA:Z:chr3,-84617448,40M,0;\tX1:i:0\tX0:i:2",
"recordGroupName": null, "recordGroupSample": null, "mateAlignmentStart":
null, "mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize":
null}); not retrying
2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 2.0 in stage 2.0 (TID 11)
had a not serializable result: org.bdgenomics.formats.avro.AlignmentRecord
Serialization stack:
object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord,
value: {"readInFragment": 0, "contigName": "chr4", "start": 181076278,
"oldPosition": null, "end": 181076318, "mapq": 25, "readName":
"NB501244AR:119:HJY3WBGXY:2:23302:26459:8305", "sequence":
"CACTGTGTTTTACTTCTATTTTAAAAAACCTGAAGGCTAT", "qual":
"EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA", "cigar": "40M", "oldCigar": null,
"basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": false,
"properPair": false, "readMapped": true, "mateMapped": false,
"failedVendorQualityChecks": false, "duplicateRead": false,
"readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment":
true, "secondaryAlignment": false, "supplementaryAlignment": false,
"mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName":
null, "recordGroupSample": null, "mateAlignmentStart": null,
"mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize": null});
not retrying
Process finished with exit code 1
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