VCFParseError: invalid INFO key

Haseeb1 · November 12, 2019, 5:39am

Im trying to write my vcf to mt after applying VEP on it and this happens.

mt = vep_app.write(‘gs://pgr-share/myfile.mt’, overwrite=True)

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 338 in stage 13.0 failed 20 times, most recent failure: Lost task 338.19 in stage 13.0 (TID 8099, hailjupy-sw-mz37.us-central1-b.c.cncd-share.internal, executor 282): is.hail.utils.HailException: promis_24k_vep_dbnsfp_qced.vcf.gz:column 402: invalid INFO key .
… gene=TTN;lofteelof=LC;SIFT_score=.;.;.;.;.;sift_pred=.;.;.;.;.;Polyphen2 …
^
offending line: 2 179396755 . G A 2600.85 PASS AC=1;AF=2.11100e-05;AN=47376;…
see the Hail log for the full offending line
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:20)
at is.hail.utils.package$.fatal(package.scala:74)
at is.hail.io.vcf.LoadVCF$$anonfun$parseLines$1$$anon$1.hasNext(LoadVCF.scala:1298)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$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:762)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
at is.hail.utils.FlipbookIterator$$anon$9.(FlipbookIterator.scala:344)
at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:63)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:155)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:152)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:108)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:104)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:104)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:103)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:103)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:101)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:101)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:99)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:97)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:97)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:836)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:834)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
at scala.collection.AbstractIterator.to(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: is.hail.io.vcf.VCFParseError: invalid INFO key .
at is.hail.io.vcf.VCFLine.parseError(LoadVCF.scala:59)
at is.hail.io.vcf.VCFLine.parseAddInfo(LoadVCF.scala:953)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1361)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$15.apply(LoadVCF.scala:1592)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$15.apply(LoadVCF.scala:1592)
at is.hail.io.vcf.LoadVCF$$anonfun$parseLines$1$$anon$1.hasNext(LoadVCF.scala:1276)
… 79 more
is.hail.utils.HailException: promis_24k_vep_dbnsfp_qced.vcf.gz:column 402: invalid INFO key .
… gene=TTN;lofteelof=LC;SIFT_score=.;.;.;.;.;sift_pred=.;.;.;.;.;Polyphen2 …
^
offending line: 2 179396755 . G A 2600.85 PASS AC=1;AF=2.11100e-05;AN=47376;…
see the Hail log for the full offending line
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:20)
at is.hail.utils.package$.fatal(package.scala:74)
at is.hail.io.vcf.LoadVCF$$anonfun$parseLines$1$$anon$1.hasNext(LoadVCF.scala:1298)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$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:762)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
at is.hail.utils.FlipbookIterator$$anon$9.(FlipbookIterator.scala:344)
at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:63)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:155)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:152)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:108)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:104)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:104)

10:38 AM

at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:103)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:103)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:101)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:101)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:99)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:97)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:97)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:836)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:834)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
at scala.collection.AbstractIterator.to(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

10:38 AM

is.hail.io.vcf.VCFParseError: invalid INFO key .
at is.hail.io.vcf.VCFLine.parseError(LoadVCF.scala:59)
at is.hail.io.vcf.VCFLine.parseAddInfo(LoadVCF.scala:953)
at is.hail.io.vcf.LoadVCF$.parseLine(LoadVCF.scala:1361)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$15.apply(LoadVCF.scala:1592)
at is.hail.io.vcf.MatrixVCFReader$$anonfun$15.apply(LoadVCF.scala:1592)
at is.hail.io.vcf.LoadVCF$$anonfun$parseLines$1$$anon$1.hasNext(LoadVCF.scala:1276)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$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:762)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDRegionValue$$anonfun$boundary$extension$1$$anon$1.hasNext(RichContextRDDRegionValue.scala:186)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:22)
at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
at is.hail.utils.FlipbookIterator$$anon$9.(FlipbookIterator.scala:344)
at is.hail.utils.FlipbookIterator.leftJoinDistinct(FlipbookIterator.scala:323)
at is.hail.annotations.OrderedRVIterator.leftJoinDistinct(OrderedRVIterator.scala:63)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$6.apply(KeyedRVD.scala:145)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:155)
at is.hail.rvd.KeyedRVD$$anonfun$orderedJoinDistinct$1.apply(KeyedRVD.scala:152)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$czipPartitions$1$$anonfun$apply$38.apply(ContextRDD.scala:507)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32$$anonfun$apply$33.apply(ContextRDD.scala:448)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:108)

new messages

10:39 AM

at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3$$anonfun$apply$4.apply(RichContextRDDRegionValue.scala:104)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:104)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2$$anonfun$apply$3.apply(RichContextRDDRegionValue.scala:103)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:103)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(RichContextRDDRegionValue.scala:101)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:101)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2$$anonfun$apply$1.apply(RichContextRDDRegionValue.scala:99)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:97)
at is.hail.utils.package$.using(package.scala:596)
at is.hail.io.fs.HadoopFS.writeFile(HadoopFS.scala:404)
at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:97)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:836)
at is.hail.rvd.RVD$$anonfun$23.apply(RVD.scala:834)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$32.apply(ContextRDD.scala:448)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at is.hail.sparkextras.ContextRDD$$anonfun$run$1$$anonfun$apply$8.apply(ContextRDD.scala:218)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
at scala.collection.AbstractIterator.to(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Hail version: 0.2.23-aaf52cafe5ef
Error summary: VCFParseError: invalid INFO key .

tpoterba · November 12, 2019, 10:49am

I think this VCF is malformatted:

gene=TTN;lofteelof=LC;SIFT_score=.;.;.;.;.;sift_pred=.;.;.;.;.;
                                   ^

An entire INFO field key can’t be .. Something like FOO=. is fine (though preferred to leave FOO out if the value is missing).

Is it possible that this VCF came from a tool that used semicolon as a delimiter within SIFT_score? That may be the culprit.

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VCFParseError: invalid INFO key

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