If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GenomeStrip query : SVDiscoveryWalker null pointer error

shazeshaze University of the WitwatersrandMember

Dear all

We've run into a problem when running the SV Discovery Step. The problem is likely to be something we did wrong a prior step and we'd be very grateful for any advice on trying to work out where the problem came from.

At this point we're just using the test data in the svtoolkit installtest directory and the GATK version in that

This is the error message:

INFO  11:55:32,442 HelpFormatter - Program Args: -T SVDiscoveryWalker -R /home/user/GS_commands//data/human_b36_chr1.fasta -O installtest-unfilter.vcf -disableGATKTraversal true -md /home/user/GS_commands/metadata -configFile /home/user/GS_commands/conf/genstrip_installtest_parameters.txt -runDirectory /home/user/GS_commands/ -genderMapFile /home/user/GS_commands//data/ -genomeMaskFile /home/user/GS_commands//data/human_b36_chr1.svmask.fasta -L 1 -runFilePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 -storeReadPairFile true 
INFO  11:55:32,446 HelpFormatter - Executing as [email protected] on Linux 3.10.0-862.9.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_181-b13. 
INFO  11:55:32,447 HelpFormatter - Date/Time: 2018/10/25 11:55:32 
INFO  11:55:32,447 HelpFormatter - ----------------------------------------------------------------------------------------- 
INFO  11:55:32,447 HelpFormatter - ----------------------------------------------------------------------------------------- 
INFO  11:55:32,455 25-Oct-2018 GenomeAnalysisEngine - Strictness is SILENT
INFO  11:55:37,311 25-Oct-2018 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO  11:55:37,332 25-Oct-2018 IntervalUtils - Processing 247249719 bp from intervals
INFO  11:55:37,401 25-Oct-2018 GenomeAnalysisEngine - Preparing for traversal
INFO  11:55:37,412 25-Oct-2018 GenomeAnalysisEngine - Done preparing for traversal
INFO  11:55:37,413 25-Oct-2018 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  11:55:37,413 25-Oct-2018 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
INFO  11:55:37,416 25-Oct-2018 SVDiscovery - Initializing SVDiscovery ...
INFO  11:55:37,416 25-Oct-2018 SVDiscovery - Reading configuration file ...
INFO  11:55:37,422 25-Oct-2018 SVDiscovery - Read configuration file.
INFO  11:55:37,423 25-Oct-2018 SVDiscovery - Opening reference sequence ...
INFO  11:55:37,424 25-Oct-2018 SVDiscovery - Opened reference sequence.
INFO  11:55:37,424 25-Oct-2018 SVDiscovery - Opening genome mask ...
INFO  11:55:37,425 25-Oct-2018 SVDiscovery - Opened genome mask.
INFO  11:55:37,425 25-Oct-2018 SVDiscovery - Initializing input data set ...
INFO  11:55:37,485 25-Oct-2018 SVDiscovery - Initialized data set: 1 file, 900 read groups, 45 samples.
INFO  11:55:37,487 25-Oct-2018 MetaData - Opening metadata ... 
INFO  11:55:37,487 25-Oct-2018 MetaData - Adding metadata location /home/user/GS_commands/metadata ...
INFO  11:55:37,489 25-Oct-2018 MetaData - Opened metadata.
INFO  11:55:37,494 25-Oct-2018 SVDiscovery - Opened metadata.
INFO  11:55:37,502 25-Oct-2018 MetaData - Loading insert size histograms ...
INFO  11:55:37,632 25-Oct-2018 SVDiscovery - Processing locus: 1:0-0:100-1000000
INFO  11:55:37,632 25-Oct-2018 SVDiscovery - Locus search window: 1:0-0
INFO  11:55:44,199 25-Oct-2018 SVDiscovery - Discovery alt home filtering is disabled.
INFO  11:55:48,158 25-Oct-2018 SVDiscovery - Processing clusters ...
##### ERROR --
##### ERROR stack trace 
    at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
##### 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
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)

The command we execute is

java -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -cp /opt/exp_soft/bioinf/svtoolkit/lib/SVToolkit.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/Queue.jar  -cp /opt/exp_soft/bioinf/svtoolkit/lib/SVToolkit.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/opt/exp_soft/bioinf/svtoolkit/lib/gatk/Queue.jar -T SVDiscoveryWalker -R /home/user/GS_commands//data/human_b36_chr1.fasta -I installtest.bam               -O installtest-unfilter.vcf  -disableGATKTraversal true  -md /home/user/GS_commands/metadata  -configFile /home/user/GS_commands/conf/genstrip_installtest_parameters.txt              -runDirectory /home/user/GS_commands/  -genderMapFile /home/user/GS_commands//data/           -genomeMaskFile /home/user/GS_commands//data/human_b36_chr1.svmask.fasta               -L 1  -runFilePrefix test1  -searchLocus 1  -searchWindow 1  -searchMinimumSize 100          -searchMaximumSize 1000000  -storeReadPairFile true

Many thanks for any help


Sign In or Register to comment.