org.broadinstitute.hellbender.exceptions.UserException

A USER ERROR has occurred: Failed to read bam header from gs://sv-data-dsde-dev/test_data/smallCram.cram Caused by:null


Solutions on the web3

Solution icon of github
A USER ERROR has occurred: Failed to read bam header from gs://sv-data-dsde-dev/test_data/smallCram.cram Caused by:null

Solution icon of github
via GitHub by tomwhite
, 8 months ago
A USER ERROR has occurred: Failed to read bam header from gs://hellbender/test/resources/benchmark/CEUTrio.HiSeq.WEx.b37.NA12892.bam Caused by:Error reading null at position 0

Solution icon of github
via GitHub by mwalker174
, 6 months ago
A USER ERROR has occurred: Failed to read bam header from gs://mw-pathseq-test/hs37d5cs.reads.sorted.bam Caused by:Error reading null at position 0

Stack trace

  • org.broadinstitute.hellbender.exceptions.UserException: A USER ERROR has occurred: Failed to read bam header from gs://sv-data-dsde-dev/test_data/smallCram.cram Caused by:null at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getHeader(ReadsSparkSource.java:182) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReads(GATKSparkTool.java:381) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:361) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:351) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:112) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:96) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:103) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:116) at org.broadinstitute.hellbender.Main.main(Main.java:158) 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 org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) Caused by: java.lang.NullPointerException at java.io.ByteArrayInputStream.<init>(ByteArrayInputStream.java:106) at org.broadinstitute.hellbender.engine.AuthHolder.getOfflineAuth(AuthHolder.java:79) at org.broadinstitute.hellbender.engine.AuthHolder.makeStorageClient(AuthHolder.java:94) at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getHeader(ReadsSparkSource.java:177) ... 20 more

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