hello,
Any idea why the following code fires the below error?
hc = HailContext()
vds = hc.read(‘gs://data_gnomad_orielresearch/gnomad.exomes.r2.0.1.sites.Y.vds’)
vds.export_vcf(“gs://data_gnomad_orielresearch/vdsToCSV.vcf”)
Many thanks,
eilalan
vds.export_vcf
Traceback (most recent call last):
File “/tmp/210fef62-20c6-4810-a199-10570b413a00/convertVDSToCSV_variant.py”, line 17, in
vds.export_vcf(“gs://data_gnomad_orielresearch/vdsToCSV.vcf”)
File “”, line 2, in export_vcf
File “/home/ec2-user/BuildAgent/work/c38e75e72b769a7c/python/hail/java.py”, line 113, in handle_py4j
hail.java.FatalError: HailException: Cannot export type `Set[String]’ to VCF INFO field.
Java stack trace:
is.hail.utils.HailException: Cannot export type `Set[String]’ to VCF INFO field.
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:6)
at is.hail.utils.package$.fatal(package.scala:25)
at is.hail.io.vcf.ExportVCF$.infoType(ExportVCF.scala:98)
at is.hail.io.vcf.ExportVCF$$anonfun$header$1$4$$anonfun$apply$8.apply(ExportVCF.scala:301)
at is.hail.io.vcf.ExportVCF$$anonfun$header$1$4$$anonfun$apply$8.apply(ExportVCF.scala:295)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
at is.hail.io.vcf.ExportVCF$$anonfun$header$1$4.apply(ExportVCF.scala:295)
at is.hail.io.vcf.ExportVCF$$anonfun$header$1$4.apply(ExportVCF.scala:295)
at scala.Option.foreach(Option.scala:257)
at is.hail.io.vcf.ExportVCF$.header$1(ExportVCF.scala:295)
at is.hail.io.vcf.ExportVCF$.apply(ExportVCF.scala:429)
at is.hail.variant.VariantDatasetFunctions$.exportVCF$extension(VariantDataset.scala:622)
at is.hail.variant.VariantDatasetFunctions.exportVCF(VariantDataset.scala:622)
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:237)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:745)
Hail version: 0.1-cf0e013
Error summary: HailException: Cannot export type `Set[String]’ to VCF INFO field.
ERROR: (gcloud.dataproc.jobs.submit.pyspark) Job [210fef62-20c6-4810-a199-10570b413a00] entered state [ERROR] while waiting for [DONE].