Hi,
I have a question when running HaplotypeCaller functions with intervals on exome-seq data.
Here is the command I used:
java -jar gatk-package-4.0.6.0-local.jar HaplotypeCaller -R /espresso/share/genomes/hg38/genome.fa -I recal_reads.bam -O variants.g.vcf -ERC GVCF -L capture.bed
However, when I ran the command, I got the following message:
17:13:14.439 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:13:14.591 INFO HaplotypeCaller - ------------------------------------------------------------ 17:13:14.591 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.6.0 17:13:14.591 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:13:14.591 INFO HaplotypeCaller - Executing as ... on Linux v2.6.32-431.29.2.el6.x86_64 amd64 17:13:14.592 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13 17:13:14.592 INFO HaplotypeCaller - Start Date/Time: July 16, 2018 5:13:14 PM EDT 17:13:14.592 INFO HaplotypeCaller - ------------------------------------------------------------ 17:13:14.592 INFO HaplotypeCaller - ------------------------------------------------------------ 17:13:14.592 INFO HaplotypeCaller - HTSJDK Version: 2.16.0 17:13:14.592 INFO HaplotypeCaller - Picard Version: 2.18.7 17:13:14.592 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:13:14.592 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:13:14.592 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:13:14.592 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:13:14.593 INFO HaplotypeCaller - Deflater: IntelDeflater 17:13:14.593 INFO HaplotypeCaller - Inflater: IntelInflater 17:13:14.593 INFO HaplotypeCaller - GCS max retries/reopens: 20 17:13:14.593 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 17:13:14.593 INFO HaplotypeCaller - Initializing engine 17:13:15.037 INFO FeatureManager - Using codec BEDCodec to read file file:///capture.bed 17:13:16.883 INFO IntervalArgumentCollection - Processing 64190747 bp from intervals 17:13:17.009 INFO HaplotypeCaller - Shutting down engine [July 16, 2018 5:13:17 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=2041053184 java.lang.NullPointerException at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325) at java.util.ComparableTimSort.sort(ComparableTimSort.java:202) at java.util.Arrays.sort(Arrays.java:1312) at java.util.Arrays.sort(Arrays.java:1506) at java.util.ArrayList.sort(ArrayList.java:1454) at java.util.Collections.sort(Collections.java:141) at org.broadinstitute.hellbender.utils.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:459) at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:956) at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:971) at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.<init>(MultiIntervalLocalReadShard.java:59) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.makeReadShards(AssemblyRegionWalker.java:195) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:175) 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)
I did not see any error but it seems HaplotypeCaller did not run and there is no output.
So I will really appreciate it if I can get help from you guys.
Thank you!
Best,
Siyu