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Issue of Haplotype call on a large chromosome (>536 Mb)

Hi
I tried to run HaplotypeCaller with GVCF mode. My reference genome is over 5 Gb in size. Below my code and error,

Using GATK jar /source/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -XX:+UseSerialGC -Xmx100g -jar /source/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar HaplotypeCaller -R /data/Pseudomolecule_v3.fasta -L /IntervalFiles/0003-scattered.intervals -I WGS_FTNO.cram -O result/0003-scattered.vcf.gz -mbq 20 --native-pair-hmm-threads 4 -ERC GVCF --verbosity ERROR
[August 1, 2018 11:32:11 AM CEST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2076049408
htsjdk.samtools.SAMException: Exception creating BAM index for slice slice: seqID 1, start 536834320, span 457789, records 259850.
at htsjdk.samtools.CRAMBAIIndexer.processSingleReferenceSlice(CRAMBAIIndexer.java:194)
at htsjdk.samtools.cram.CRAIIndex.openCraiFileAsBaiStream(CRAIIndex.java:180)
at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:78)
at htsjdk.samtools.CRAMFileReader.initWithStreams(CRAMFileReader.java:228)
at htsjdk.samtools.CRAMFileReader.(CRAMFileReader.java:219)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:422)
at htsjdk.samtools.SamReaderFactory.open(SamReaderFactory.java:105)
at org.broadinstitute.hellbender.engine.ReadsDataSource.(ReadsDataSource.java:227)
at org.broadinstitute.hellbender.engine.ReadsDataSource.(ReadsDataSource.java:162)
at org.broadinstitute.hellbender.engine.GATKTool.initializeReads(GATKTool.java:387)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:636)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:156)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:133)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 32770
at htsjdk.samtools.CRAMBAIIndexer$BAMIndexBuilder.processSingleReferenceSlice(CRAMBAIIndexer.java:354)
at htsjdk.samtools.CRAMBAIIndexer$BAMIndexBuilder.access$100(CRAMBAIIndexer.java:227)
at htsjdk.samtools.CRAMBAIIndexer.processSingleReferenceSlice(CRAMBAIIndexer.java:192)
... 17 more

Does GATK4 handle large single chromosome ? Is there any solution ?

Answers

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