Feature request: helpful error messages for file lists

TechnicalVaultTechnicalVault Cambridge, UKMember ✭✭✭

One of the files or indices in my input file list is corrupt, unfortunately because of the error message yielded it's hard to tell which specific file it is. Could more useful error messages be added to the todo list?

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.RuntimeException: java.io.IOException: Unexpected compressed block length: 1
        at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:45)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:147)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:135)
        at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:110)
        at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
        at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
        at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
        at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
        at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
        at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.<init>(RodLocusView.java:83)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.io.IOException: Unexpected compressed block length: 1
        at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:377)
        at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:292)
        at htsjdk.tribble.readers.TabixReader$Iterator.next(TabixReader.java:339)
        at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:43)
        ... 18 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: java.io.IOException: Unexpected compressed block length: 1
##### ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

Sign In or Register to comment.