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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

What does "ERROR MESSAGE: Cannot enable index memory mapping for a SAM text reader" mean?

I have used indelrealinger sucessfully in the past but I am now getting the following error. Please let me know if you have any suggestions.

[Fri Feb 15 09:09:37 GMT 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/exports/home/fturner/vet_roslin_ark_genomics/reference_gen
omes/chicken/Gallus_gallus.WASHUC2.69.dna.toplevel.fa OUTPUT=/exports/home/fturner/vet_roslin_ark_genomics/reference_genomes/chicken/dict129865
[Fri Feb 15 09:09:37 GMT 2013] Executing as fturner@eddie327 on Linux 2.6.32-220.23.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0
[Fri Feb 15 09:09:52 GMT 2013] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.24 minutes.

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.UnsupportedOperationException: Cannot enable index memory mapping for a SAM text reader
at net.sf.samtools.SAMTextReader.enableIndexMemoryMapping(
at net.sf.samtools.SAMFileReader.enableIndexMemoryMapping(
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMReaders.(
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.createNewResource(
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.getAvailableReaders(
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.createReadsDataSource(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.1-23-g8072bd9):
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Cannot enable index memory mapping for a SAM text reader


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