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Better error messages from GATK

One minor change that would make GATK much easier to use with large data sets would be if GATK could provide slightly more detailed error messages, specifically for the cases where the error is related to a specific file.

For example the following Error message tells me one of my GVCF files has been damaged/corrupted at some point but doesn't tell me which one it is which is rather important information as as a result I now have to work my way through ~30files to work out which one is damaged and replace it with a good copy. While if GATK had provided the file name along with the error I would have been able to directly go to the file and replace it.

This has been a problem with the GVCF, VCF, & BAM files, and it would be greatly appreciated if it could be changed!

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$FeatureIterator.readNextRecord(TabixFeatureReader.java:161)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.(TabixFeatureReader.java:149)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:124)
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.(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.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
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$IteratorImpl.next(TabixReader.java:382)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:43)
... 18 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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 MESSAGE: java.io.IOException: Unexpected compressed block length: 1
ERROR ------------------------------------------------------------------------------------------

Issue · Github
by Geraldine_VdAuwera

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