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