# HailException: invalid interval expression **URL:** \ **Category:** Help \[0.1\]\ **Created:** [July 31, 2018, 8:29pm UTC](https://discuss.hail.is/t/hailexception-invalid-interval-expression/591 "2018-07-31T20:29:00Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Laura](https://avatars.discourse-cdn.com/v4/letter/l/a4c791/32.png) [@Laura](https://discuss.hail.is/u/Laura)\ **Post date:** [July 31, 2018, 8:29pm UTC](https://discuss.hail.is/t/hailexception-invalid-interval-expression/591/1 "2018-07-31T20:29:00Z")
Hi, When I try to filter my mt file like this ds = hl.filter\_intervals(vds,[hl.parse\_locus\_interval(x) for x in [‘20-22’]], keep=True) I got this error: HailException: invalid interval expression: `20-22’. The genome reference for my dataset is GRCh38, so I initialized Hail like this: hl.init(default\_reference=‘GRCh38’). I did this filter in other dataset and I didn’t get this error (the others had GRCh37 as reference genome). FatalError Traceback (most recent call last) in () ----\> 1 vds = hl.filter\_intervals(vds,[hl.parse\_locus\_interval(x) for x in [‘20-22’]], keep=True) /home/hail/hail.zip/hail/typecheck/check.py in wrapper(\*args, \*\*kwargs) 545 def wrapper(\*args, \*\*kwargs): 546 args\_, kwargs\_ = check\_all(f, args, kwargs, checkers, is\_method=is\_method) –\> 547 return f(\*args\_, \*\*kwargs\_) 548 549 update\_wrapper(wrapper, f) /home/hail/hail.zip/hail/methods/misc.py in filter\_intervals(ds, intervals, keep) 314 return interval 315 –\> 316 intervals = [wrap\_input(x).\_jrep for x in intervals.value] 317 jmt = Env.hail().methods.FilterIntervals.apply(ds.\_jvds, intervals, keep) 318 return MatrixTable(jmt) /home/hail/hail.zip/hail/expr/expressions/base\_expression.py in value(self) 784 785 “”" –\> 786 return hl.eval\_expr(self) 787 788 def \_aggregation\_method(self): /home/hail/hail.zip/hail/typecheck/check.py in wrapper(\*args, \*\*kwargs) 545 def wrapper(\*args, \*\*kwargs): 546 args\_, kwargs\_ = check\_all(f, args, kwargs, checkers, is\_method=is\_method) –\> 547 return f(\*args\_, \*\*kwargs\_) 548 549 update\_wrapper(wrapper, f) /home/hail/hail.zip/hail/expr/expressions/expression\_utils.py in eval\_expr(expression) 135 Result of evaluating `expression`. 136 “”" –\> 137 return eval\_expr\_typed(expression)[0] 138 139 /home/hail/hail.zip/hail/typecheck/check.py in wrapper(\*args, \*\*kwargs) 545 def wrapper(\*args, \*\*kwargs): 546 args\_, kwargs\_ = check\_all(f, args, kwargs, checkers, is\_method=is\_method) –\> 547 return f(\*args\_, \*\*kwargs\_) 548 549 update\_wrapper(wrapper, f) /home/hail/hail.zip/hail/expr/expressions/expression\_utils.py in eval\_expr\_typed(expression) 169 analyze(‘eval\_expr\_typed’, expression, Indices(expression.\_indices.source)) 170 –\> 171 return expression.collect()[0], expression.dtype 172 173 /home/hail/hail.zip/hail/expr/expressions/base\_expression.py in collect(self) 767 uid = Env.get\_uid() 768 t = self.\_to\_table(uid) –\> 769 return [r[uid] for r in t.\_select(“collect”, None, hl.struct(\*\*{uid: t[uid]})).collect()] 770 771 @property /home/hail/hail.zip/hail/table.py in collect(self) 1590 List of rows. 1591 “”" -\> 1592 return hl.tarray(self.row.dtype).\_from\_json(self.\_jt.collectJSON()) 1593 1594 def describe(self): /usr/lib/spark/python/lib/py4j-0.10.4-src.zip/py4j/java\_gateway.py in **call** (self, \*args) 1131 answer = self.gateway\_client.send\_command(command) 1132 return\_value = get\_return\_value( -\> 1133 answer, self.gateway\_client, self.target\_id, self.name) 1134 1135 for temp\_arg in temp\_args: /home/hail/hail.zip/hail/utils/java.py in deco(\*args, \*\*kwargs) 198 raise FatalError(’%s\n\nJava stack trace:\n%s\n’ 199 ‘Hail version: %s\n’ –\> 200 ‘Error summary: %s’ % (deepest, full, hail. **version** , deepest)) from None 201 except pyspark.sql.utils.CapturedException as e: 202 raise FatalError(’%s\n\nJava stack trace:\n%s\n’ FatalError: HailException: invalid interval expression: `20-22’: Java stack trace: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 6.0 failed 4 times, most recent failure: Lost task 0.3 in stage 6.0 (TID 21, hail120-w-3.c.avl-hail-ines.internal, executor 3): is.hail.utils.HailException: invalid interval expression: `20-22’: at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9) at is.hail.utils.package$.fatal(package.scala:26) at is.hail.expr.Parser$.parseLocusInterval(Parser.scala:133) at is.hail.variant.Locus$.parseInterval(Locus.scala:53) at is.hail.codegen.generated.C45.method1(Unknown Source) at is.hail.codegen.generated.C45.apply(Unknown Source) at is.hail.codegen.generated.C45.apply(Unknown Source) at is.hail.expr.ir.TableMapRows$$anonfun$24$$anonfun$apply$12.apply(TableIR.scala:504) at is.hail.expr.ir.TableMapRows$$anonfun$24$$anonfun$apply$12.apply(TableIR.scala:493) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) 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$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2069) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2069) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1517) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1505) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1504) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1504) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814) at scala.Option.foreach(Option.scala:257) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1732) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1687) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1676) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2029) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2050) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2069) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2094) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:362) at org.apache.spark.rdd.RDD.collect(RDD.scala:935) at is.hail.table.Table.collect(Table.scala:655) at is.hail.table.Table.collectJSON(Table.scala:658) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:280) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:214) at java.lang.Thread.run(Thread.java:748)is.hail.utils.HailException: invalid interval expression: `20-22’: at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9) at is.hail.utils.package$.fatal(package.scala:26) at is.hail.expr.Parser$.parseLocusInterval(Parser.scala:133) at is.hail.variant.Locus$.parseInterval(Locus.scala:53) at is.hail.codegen.generated.C45.method1(Unknown Source) at is.hail.codegen.generated.C45.apply(Unknown Source) at is.hail.codegen.generated.C45.apply(Unknown Source) at is.hail.expr.ir.TableMapRows$$anonfun$24$$anonfun$apply$12.apply(TableIR.scala:504) at is.hail.expr.ir.TableMapRows$$anonfun$24$$anonfun$apply$12.apply(TableIR.scala:493) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2069) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2069) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338) 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: devel-7d33e65d8423 Error summary: HailException: invalid interval expression: `20-22’: Thanks, Laura ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [July 31, 2018, 10:37pm UTC](https://discuss.hail.is/t/hailexception-invalid-interval-expression/591/2 "2018-07-31T22:37:40Z")
Sorry these error messages aren’t great – the problem is GREATLY complicated by someone’s bright idea to allow contig names to include all sorts of things like punctuation (`:` or `-` are totally legal), meaning our interval parser is pretty complex. The problem here is that neither 20 or 22 are contigs in GRCh38 – it should be `chr20-chr22`.