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

fturnerfturner Posts: 1Member

HI
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
4176074562895.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/fturner VERBOSITY=INFO QUIET=false VALIDATION_STRI
NGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[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
_07-b10
[Fri Feb 15 09:09:52 GMT 2013] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.24 minutes.
Runtime.totalMemory()=442957824

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

java.lang.UnsupportedOperationException: Cannot enable index memory mapping for a SAM text reader
at net.sf.samtools.SAMTextReader.enableIndexMemoryMapping(SAMTextReader.java:105)
at net.sf.samtools.SAMFileReader.enableIndexMemoryMapping(SAMFileReader.java:228)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMReaders.(SAMDataSource.java:754)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.createNewResource(SAMDataSource.java:729)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.getAvailableReaders(SAMDataSource.java:700)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.(SAMDataSource.java:232)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:884)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:717)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:207)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:104)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:227)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:89)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.1-23-g8072bd9):
ERROR
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 http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Cannot enable index memory mapping for a SAM text reader
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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,364Administrator, GATK Developer admin

    Hi there,

    The version you are using is downright ancient and no longer supported... Please upgrade to the latest version.

    Geraldine Van der Auwera, PhD

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