# Liftover Range Exception and Support for chrom 'MT' **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [September 6, 2019, 3:32pm UTC](https://discuss.hail.is/t/liftover-range-exception-and-support-for-chrom-mt/1074 "2019-09-06T15:32:32Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Aditya](https://avatars.discourse-cdn.com/v4/letter/a/df705f/32.png) [@Aditya](https://discuss.hail.is/u/Aditya)\ **Post date:** [September 6, 2019, 3:32pm UTC](https://discuss.hail.is/t/liftover-range-exception-and-support-for-chrom-mt/1074/1 "2019-09-06T15:32:32Z")
Hi Team, We were trying to use Hail Liftover on DBSNP for GRCH38 to GRCH37 conversion. We faced couple of exceptions: Below is the code being used: rg37 = hl.get\_reference(‘GRCh37’) rg38 = hl.get\_reference(‘GRCh38’) rg38.add\_liftover('gs://hail-common/references/grch38\_to\_grch37.over.chain.gz, rg37) ht = ht.annotate(new\_pos=hl.liftover(hl.locus(‘chr’ + ht.chrom,ht.position, ‘GRCh38’), ‘GRCh37’)) 1. Error summary: HailException: Invalid locus `chrMT:8869' found. Contig`chrMT’ is not in the reference genome `GRCh38’. 2. Error summary: HailException: Invalid locus `chr2:242753619' found. Position`242753619’ is not within the range [1-242193529] for reference genome `GRCh38’. Seems like Chrom “MT” is not supported fro lift over. And possibly there is a range limit as well for the positions. Can you please if there is a work around for it? **More Details on the error:** File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/pyspark.zip/pyspark/sql/context.py”, line 384, in sql return self.sparkSession.sql(sqlQuery) File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/pyspark.zip/pyspark/sql/session.py”, line 556, in sql return DataFrame(self.\_jsparkSession.sql(sqlQuery), self.\_wrapped) File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/py4j-0.10.4-src.zip/py4j/java\_gateway.py”, line 1133, in **call** answer, self.gateway\_client, self.target\_id, self.name) File “/GWD/RDIP/apps/hail\_pipeline\_api/hail\_0.2/hail-python\_6942d09.zip/hail/utils/java.py”, line 196, in deco ‘Error summary: %s’ % (deepest, full, hail. **version** , deepest)) from None hail.utils.java.FatalError: HailException: Invalid locus `chr2:242753619' found. Position`242753619’ is not within the range [1-242193529] for reference genome `GRCh38’. Java stack trace: org.apache.spark.SparkException: Job aborted. at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:215) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:145) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116) at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92) at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92) at org.apache.spark.sql.hive.execution.CreateHiveTableAsSelectCommand.run(CreateHiveTableAsSelectCommand.scala:81) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:67) at org.apache.spark.sql.Dataset.(Dataset.scala:182) at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:67) at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:623) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:280) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:214) at java.lang.Thread.run(Thread.java:748)org.apache.spark.SparkException: Job aborted due to stage failure: Task 73 in stage 0.0 failed 4 times, most recent failure: Lost task 73.3 in stage 0.0 (TID 130, [us1salxhpw0300.corpnet2.com](http://us1salxhpw0300.corpnet2.com), executor 18): org.apache.spark.SparkException: Task failed while writing rows at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:272) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:191) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:190) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: is.hail.utils.HailException: Invalid locus `chr2:242753619' found. Position`242753619’ is not within the range [1-242193529] for reference genome `GRCh38’. at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9) at is.hail.utils.package$.fatal(package.scala:26) at is.hail.variant.ReferenceGenome.checkLocus(ReferenceGenome.scala:228) at is.hail.variant.Locus$.apply(Locus.scala:18) at is.hail.expr.FunctionRegistry$$anonfun$143$$anonfun$apply$86.apply(FunctionRegistry.scala:869) at is.hail.expr.FunctionRegistry$$anonfun$143$$anonfun$apply$86.apply(FunctionRegistry.scala:869) at is.hail.expr.BinaryFun.apply(Fun.scala:122) at is.hail.codegen.generated.C0.apply(Unknown Source) at is.hail.codegen.generated.C0.apply(Unknown Source) at is.hail.expr.CM$$anonfun$runWithDelayedValues$1.apply(CM.scala:84) at is.hail.expr.CM$$anonfun$runWithDelayedValues$1.apply(CM.scala:82) at is.hail.expr.Parser$$anonfun$is$hail$expr$Parser$$evalNoTypeCheck$1.apply(Parser.scala:64) at is.hail.table.Table$$anonfun$18.apply(Table.scala:576) at is.hail.table.Table$$anonfun$18.apply(Table.scala:574) at scala.collection.Iterator$$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$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$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$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.next(SerDeUtil.scala:121) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.next(SerDeUtil.scala:112) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.foreach(SerDeUtil.scala:112) at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:509) at org.apache.spark.api.python.PythonRunner$WriterThread$$anonfun$run$3.apply(PythonRDD.scala:333) at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1954) at org.apache.spark.api.python.PythonRunner$WriterThread.run(PythonRDD.scala:269) Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486) 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:1714) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630) at org.apache.spark.SparkContext.runJob(SparkContext.scala:2024) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:188) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:145) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116) at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92) at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92) at org.apache.spark.sql.hive.execution.CreateHiveTableAsSelectCommand.run(CreateHiveTableAsSelectCommand.scala:81) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:67) at org.apache.spark.sql.Dataset.(Dataset.scala:182) at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:67) at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:623) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:280) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:214) at java.lang.Thread.run(Thread.java:748)org.apache.spark.SparkException: Task failed while writing rows at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:272) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:191) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:190) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)is.hail.utils.HailException: Invalid locus `chr2:242753619' found. Position`242753619’ is not within the range [1-242193529] for reference genome `GRCh38’. at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9) at is.hail.utils.package$.fatal(package.scala:26) at is.hail.variant.ReferenceGenome.checkLocus(ReferenceGenome.scala:228) at is.hail.variant.Locus$.apply(Locus.scala:18) at is.hail.expr.FunctionRegistry$$anonfun$143$$anonfun$apply$86.apply(FunctionRegistry.scala:869) at is.hail.expr.FunctionRegistry$$anonfun$143$$anonfun$apply$86.apply(FunctionRegistry.scala:869) at is.hail.expr.BinaryFun.apply(Fun.scala:122) at is.hail.codegen.generated.C0.apply(Unknown Source) at is.hail.codegen.generated.C0.apply(Unknown Source) at is.hail.expr.CM$$anonfun$runWithDelayedValues$1.apply(CM.scala:84) at is.hail.expr.CM$$anonfun$runWithDelayedValues$1.apply(CM.scala:82) at is.hail.expr.Parser$$anonfun$is$hail$expr$Parser$$evalNoTypeCheck$1.apply(Parser.scala:64) at is.hail.table.Table$$anonfun$18.apply(Table.scala:576) at is.hail.table.Table$$anonfun$18.apply(Table.scala:574) 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$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$12.next(Iterator.scala:444) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.next(SerDeUtil.scala:121) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.next(SerDeUtil.scala:112) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.foreach(SerDeUtil.scala:112) at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:509) at org.apache.spark.api.python.PythonRunner$WriterThread$$anonfun$run$3.apply(PythonRDD.scala:333) at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1954) at org.apache.spark.api.python.PythonRunner$WriterThread.run(PythonRDD.scala:269) File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/pyspark.zip/pyspark/sql/context.py”, line 384, in sql return self.sparkSession.sql(sqlQuery) File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/pyspark.zip/pyspark/sql/session.py”, line 556, in sql return DataFrame(self.\_jsparkSession.sql(sqlQuery), self.\_wrapped) File “/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/py4j-0.10.4-src.zip/py4j/java\_gateway.py”, line 1133, in **call** answer, self.gateway\_client, self.target\_id, self.name) File “/GWD/RDIP/apps/hail\_pipeline\_api/hail\_0.2/hail-python\_6942d09.zip/hail/utils/java.py”, line 196, in deco ‘Error summary: %s’ % (deepest, full, hail. **version** , deepest)) from None hail.utils.java.FatalError: HailException: Invalid locus `chrMT:9127' found. Contig`chrMT’ is not in the reference genome `GRCh38’. Java stack trace: org.apache.spark.SparkException: Job aborted. at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:215) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:173) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:145) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116) at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92) at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92) at org.apache.spark.sql.hive.execution.CreateHiveTableAsSelectCommand.run(CreateHiveTableAsSelectCommand.scala:81) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56) at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:67) at org.apache.spark.sql.Dataset.(Dataset.scala:182) at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:67) at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:623) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:280) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:214) at java.lang.Thread.run(Thread.java:748)org.apache.spark.SparkException: Job aborted due to stage failure: Task 7 in stage 0.0 failed 4 times, most recent failure: Lost task 7.3 in stage 0.0 (TID 58, [us1salxhpw0399.corpnet2.com](http://us1salxhpw0399.corpnet2.com), executor 5): org.apache.spark.SparkException: Task failed while writing rows at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:272) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:191) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$apply$mcV$sp$1.apply(FileFormatWriter.scala:190) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$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) Caused by: is.hail.utils.HailException: Invalid locus `chrMT:9127' found. Contig`chrMT’ is not in the reference genome `GRCh38’. Thanks and Regards, Aditya Pandit ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [September 7, 2019, 8:28pm UTC](https://discuss.hail.is/t/liftover-range-exception-and-support-for-chrom-mt/1074/2 "2019-09-07T20:28:04Z")
GRCh38 does not have a contig named `chrMT`, they decided to name it `chrM`. You’ll need to update your `ht.chrom` field to change `chrMT` to `chrM`, for example using [`ht.chrom.replace(..., ...)`](https://hail.is/docs/0.2/expressions.html?highlight=replace#hail.expr.expressions.StringExpression.replace) We store contig metadata in a JSON format here: [https://github.com/hail-is/hail/blob/master/hail/src/main/resources/reference/grch38.json](https://github.com/hail-is/hail/blob/master/hail/src/main/resources/reference/grch38.json) . ---
**Author:** ![Aditya](https://avatars.discourse-cdn.com/v4/letter/a/df705f/32.png) [@Aditya](https://discuss.hail.is/u/Aditya)\ **Post date:** [September 9, 2019, 2:17pm UTC](https://discuss.hail.is/t/liftover-range-exception-and-support-for-chrom-mt/1074/3 "2019-09-09T14:17:15Z")
> [@danking](#): > > etadata in a JSON format Hi Danking, Thanks for your advise on this. Handling chrMT as chrM did solve that issue. However we are still unsure on the exception for position range. Can you share your thoughts on that please. ---
**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:** [September 9, 2019, 2:18pm UTC](https://discuss.hail.is/t/liftover-range-exception-and-support-for-chrom-mt/1074/4 "2019-09-09T14:18:38Z")
242753619 is a position larger than the length of chromosome 2, so it’s got to be invalid. I’d check with whoever generated this VCF for you.