Hail: VCFParseError

krithika_s · March 19, 2021, 10:17am

Hi,

I am currently working on Variant Quality Checks of vcf file using Hail. I am getting the below error. Kindly help to resolve this issue.

Hail version: 0.2.61-3c86d3ba497a
Error summary: VCFParseError: invalid character ‘|’ in integer literal

Thanks in advance

tpoterba · March 19, 2021, 3:51pm

This means your VCF is malformed. I bet that the problem is an incorrect header – a field designated with Number=1 that’s actually an array (number=A,R,G,2+, etc) in the data.

krithika_s · March 19, 2021, 4:17pm

Thanks for your reply… I have used each chromosome vcf files for variant QC, I didn’t get this error. And then I merged all chromosomes to one vcf file using gatk merge vcf, this merged vcf had throwing this error.

But this same excerise I have performed before, I didn’t face this issues. But now I am getting this error.

Could you please help me how can I fix this issue?

tpoterba · March 19, 2021, 4:21pm

what’s the full stack trace?

krithika_s · March 22, 2021, 6:52am

p1 = hl.plot.histogram(qc_table.gq_mean, range=(10,80), legend=‘Variant Mean GQ’)
[Stage 5:> (0 + 72) / 8050]Traceback (most recent call last):
File “”, line 1, in
File “”, line 2, in histogram
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/typecheck/check.py”, line 614, in wrapper
return original_func(*args, **kwargs)
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/plot/plots.py”, line 401, in histogram
data = agg_f(aggregators.hist(data, start, end, bins))
File “”, line 2, in aggregate
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/typecheck/check.py”, line 614, in wrapper
return original_func(*args, **kwargs)
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/table.py”, line 1178, in aggregate
return Env.backend().execute(agg_ir)
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/backend/py4j_backend.py”, line 98, in execute
raise e
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/backend/py4j_backend.py”, line 74, in execute
result = json.loads(self._jhc.backend().executeJSON(jir))
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/py4j/java_gateway.py”, line 1257, in call
answer, self.gateway_client, self.target_id, self.name)
File “/gpfs/data/user/krithika/soft/miniconda3/envs/gatk_m/lib/python3.6/site-packages/hail/backend/py4j_backend.py”, line 32, in deco
‘Error summary: %s’ % (deepest, full, hail.version, deepest), error_id) from None
hail.utils.java.FatalError: VCFParseError: invalid character ‘|’ in integer literal

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 68 in stage 5.0 failed 1 times, most recent failure: Lost task 68.0 in stage 5.0 (TID 24619, localhost, executor driver): is.hail.utils.HailException: file:/gpfs/data/user/krithika/G9_G13/GenomeIndia_vcf/Trail/651_allchr_merge.vcf:offset 9127150159: error while parsing line
chr1 21955383 . CGGGTGGG GGGGTGGG,CGGGGTGGG,* 475.51 . AC=12,4,14;AF=0.013,4.255e-03,0.015;AN=940;AS_UNIQ_ALT_READ_COUNT=0|0|0;BaseQRankSum=-1.176e+00;DP=23940;ExcessHet=0.0053;FS=186.849;GQ_MEAN=11.31;GQ_STDDEV=22.92;InbreedingCoeff=0.0556;MBQ=0,0,0,0;MFRL=0,0,0,0;MLEAC=14,24,52;MLEAF=0.015,0.026,0.055;MMQ=60,60,60,60;MPOS=50,50,50;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=181;NCount=0;QD=1.23;ReadPosRankSum=-1.553e+00;SOR=9.230 GT:AD:AF:DP:F1R2:F2R1:GQ:PGT:PID:PL:PS ./.:35,0,0,0:.:35:0,0,0,0:0,0,0,0:.:.:.:0,0,0,0,0,0,0,0,0,0

at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:15)
at is.hail.utils.package$.fatal(package.scala:77)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1745)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1734)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:68)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Caused by: is.hail.io.vcf.VCFParseError: invalid character ‘|’ in integer literal
at is.hail.io.vcf.VCFLine.parseError(LoadVCF.scala:59)
at is.hail.io.vcf.VCFLine.numericValue(LoadVCF.scala:63)
at is.hail.io.vcf.VCFLine.parseIntInInfoArray(LoadVCF.scala:810)
at is.hail.io.vcf.VCFLine.parseIntInfoArrayElement(LoadVCF.scala:831)
at is.hail.io.vcf.VCFLine.parseAddInfoArrayInt(LoadVCF.scala:855)
at is.hail.io.vcf.VCFLine.parseAddInfoField(LoadVCF.scala:933)
at is.hail.io.vcf.VCFLine.addInfoField(LoadVCF.scala:953)
at is.hail.io.vcf.VCFLine.parseAddInfo(LoadVCF.scala:986)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1428)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1304)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1741)
… 42 more

Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2158)
at is.hail.rvd.RVD.combine(RVD.scala:724)
at is.hail.expr.ir.Interpret$.run(Interpret.scala:938)
at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:354)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:338)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:335)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:25)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:23)
at is.hail.utils.package$.using(package.scala:618)
at is.hail.annotations.Region$.scoped(Region.scala:18)
at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:23)
at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:247)
at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:335)
at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:379)
at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:377)
at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)
at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:377)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)

is.hail.utils.HailException: file:/gpfs/data/user/krithika/G9_G13/GenomeIndia_vcf/Trail/651_allchr_merge.vcf:offset 9127150159: error while parsing line
chr1 21955383 . CGGGTGGG GGGGTGGG,CGGGGTGGG,* 475.51 . AC=12,4,14;AF=0.013,4.255e-03,0.015;AN=940;AS_UNIQ_ALT_READ_COUNT=0|0|0;BaseQRankSum=-1.176e+00;DP=23940;ExcessHet=0.0053;FS=186.849;GQ_MEAN=11.31;GQ_STDDEV=22.92;InbreedingCoeff=0.0556;MBQ=0,0,0,0;MFRL=0,0,0,0;MLEAC=14,24,52;MLEAF=0.015,0.026,0.055;MMQ=60,60,60,60;MPOS=50,50,50;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=181;NCount=0;QD=1.23;ReadPosRankSum=-1.553e+00;SOR=9.230 GT:AD:AF:DP:F1R2:F2R1:GQ:PGT:PID:PL:PS ./.:35,0,0,0:.:35:0,0,0,0:0,0,0,0:.:.:.:0,0,0,0,0,0,0,0,0,0

at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:15)
at is.hail.utils.package$.fatal(package.scala:77)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1745)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1734)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:68)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

is.hail.io.vcf.VCFParseError: invalid character ‘|’ in integer literal
at is.hail.io.vcf.VCFLine.parseError(LoadVCF.scala:59)
at is.hail.io.vcf.VCFLine.numericValue(LoadVCF.scala:63)
at is.hail.io.vcf.VCFLine.parseIntInInfoArray(LoadVCF.scala:810)
at is.hail.io.vcf.VCFLine.parseIntInfoArrayElement(LoadVCF.scala:831)
at is.hail.io.vcf.VCFLine.parseAddInfoArrayInt(LoadVCF.scala:855)
at is.hail.io.vcf.VCFLine.parseAddInfoField(LoadVCF.scala:933)
at is.hail.io.vcf.VCFLine.addInfoField(LoadVCF.scala:953)
at is.hail.io.vcf.VCFLine.parseAddInfo(LoadVCF.scala:986)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1428)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1304)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1741)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$21$$anonfun$apply$10$$anonfun$apply$11.apply(LoadVCF.scala:1734)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:464)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:68)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Hail version: 0.2.61-3c86d3ba497a
Error summary: VCFParseError: invalid character ‘|’ in integer literal
[Stage 5:> (0 + 11) / 8050]

krithika_s · March 23, 2021, 6:03am

Hi @tpoterba, could you please tell me how to fix this issues.

Hail version: 0.2.61-3c86d3ba497a
Error summary: VCFParseError: invalid character ‘|’ in integer literal
[Stage 5:> (0 + 11) / 8050]

tpoterba · March 23, 2021, 1:00pm

We can improve the error message in the future to point to the specific problematic field, but for now you should run this VCF through something like the vcftools vcf-validator, which should tell you where the problem is.

Topic		Replies	Views
Unable to write MatrixTable (VCFParseError) Hail Query & hailctl	3	370	July 20, 2022
Error summary: VCFParseError: unexpected end of line Hail Query & hailctl	4	628	May 19, 2020
Error in variant/sample QC. Malformed VCF? Hail Query & hailctl	2	373	March 23, 2021
VCF format for hail in seqr Help [0.1]	19	1291	September 19, 2018
Unable to load VCF file Hail Query & hailctl	2	399	January 27, 2022

Hail: VCFParseError

Related topics