GATK 3.8 Dictionary cannot have size zero

HoppmannHoppmann FreiburgMember

Hi,

today I wanted to update my pipeline from running on GATK3.6 to 3.8. But now it complains about the dictionary.

ERROR --
ERROR stack trace

java.lang.IllegalArgumentException: Dictionary cannot have size zero
at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.(MRUCachingSAMSequenceDictionary.java:62)
at org.broadinstitute.gatk.utils.GenomeLocParser$1.initialValue(GenomeLocParser.java:78)
at org.broadinstitute.gatk.utils.GenomeLocParser$1.initialValue(GenomeLocParser.java:75)
at java.lang.ThreadLocal.setInitialValue(ThreadLocal.java:180)
at java.lang.ThreadLocal.get(ThreadLocal.java:170)
at org.broadinstitute.gatk.utils.GenomeLocParser.getContigInfo(GenomeLocParser.java:91)
at org.broadinstitute.gatk.utils.GenomeLocParser.getContigs(GenomeLocParser.java:204)
at org.broadinstitute.gatk.utils.GenomeLocParser.(GenomeLocParser.java:135)
at org.broadinstitute.gatk.utils.GenomeLocParser.(GenomeLocParser.java:108)
at org.broadinstitute.gatk.utils.GenomeLocSortedSet.createSetFromSequenceDictionary(GenomeLocSortedSet.java:444)
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.createOverMappedReads(BAMScheduler.java:66)
at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.shardOverMappedReads(IntervalSharder.java:55)
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.createShardIteratorOverMappedReads(SAMDataSource.java:1237)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:676)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Dictionary cannot have size zero
ERROR ------------------------------------------------------------------------------------------

The command I used is basically the same I used for GATK 3.6 where it still worked this yesterday.

/dsk/localall/lib/java/jre1.8.0_131_x64/bin/java \
-Xmx10g \
-jar /data/ngs/bin/GATK/3.8.0/GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-l INFO \
-nt 4 \
-R /data/ngs/resources/bundle/2.8/ucsc.hg19.fasta \
-known /data/ngs/resources/bundle/2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf \
-known /data/ngs/resources/bundle/2.8/1000G_phase1.indels.hg19.vcf \
--filter_mismatching_base_and_quals \
--filter_bases_not_stored \
--filter_reads_with_N_cigar \
-I out/01-alignment/FG315.bam \
-o out/03-realignment/FG315/FG315.list \
-log out/03-realignment/FG315/FG315.creator.log

I've tried to google this issue and found an old forum entry on seqanswers.com where they state, that the index should be redone.
http://seqanswers.com/forums/showthread.php?t=20599

I've checked my index and it's not empty.
11K -rwxrws---+ 1 hoppmann ngs 3.5K Aug 1 16:58 /data/ngs/resources/bundle/2.8/ucsc.hg19.fasta.fai
chrM 16571 6 50 51
chr1 249250621 16915 50 51
chr2 243199373 254252555 50 51
chr3 198022430 502315922 50 51
chr4 191154276 704298807 50 51
chr5 180915260 899276175 50 51
chr6 171115067 1083809747 50 51
chr7 159138663 1258347122 50 51
chr8 146364022 1420668565 50 51
chr9 141213431 1569959874 50 51
chr10 135534747 1713997581 50 51
chr11 135006516 1852243030 50 51
...

I still did the indexing with samtools, but it didn't work.

Am I doing something wrong, or is this a bug?

Best,

Anselm Hoppmann

Best Answer

  • HoppmannHoppmann Freiburg
    Accepted Answer

    Never mind.

    It happend, that BWA crashed and there were only empty sam/bam files available...

    Would it be possible to test for this problem and make an according ERROR message? I didn't think of this option, since I found an entry in seqanswers.com handling the same ERROR message with a different origin.

    Best,

    Anselm Hoppmann

Answers

  • HoppmannHoppmann FreiburgMember
    Accepted Answer

    Never mind.

    It happend, that BWA crashed and there were only empty sam/bam files available...

    Would it be possible to test for this problem and make an according ERROR message? I didn't think of this option, since I found an entry in seqanswers.com handling the same ERROR message with a different origin.

    Best,

    Anselm Hoppmann

    Issue · Github
    by Sheila

    Issue Number
    2431
    State
    open
    Last Updated
    Assignee
    Array
    Milestone
    Array
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Hoppmann
    Hi Anselm,

    Glad you solved this on your own. I will see what the team says about making the error message more clear.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Hoppmann
    Hi Anselm,

    We will put a fix in GATK4 if it is still an issue. Can you submit a bug report? Instructions are here.

    Thanks,
    Sheila

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