Notice:
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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Runtime error in BaseRecalibrator (version 2.2-8-g99996f2)

Hi,

I got this error today running BaseRecalibrator:

ERROR stack trace

java.lang.NullPointerException
at java.util.concurrent.locks.AbstractQueuedSynchronizer.hasQueuedPredecessors(AbstractQueuedSynchronizer.java:1453)
at java.util.concurrent.locks.ReentrantLock$FairSync.tryAcquire(ReentrantLock.java:240)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireInterruptibly(AbstractQueuedSynchronizer.java:1158)
at java.util.concurrent.locks.ReentrantLock.lockInterruptibly(ReentrantLock.java:340)
at java.util.concurrent.PriorityBlockingQueue.take(PriorityBlockingQueue.java:244)
at org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceAsMuchAsPossible(Reducer.java:121)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:510)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:636)

The command arguments I used are:
-nct 4 -T BaseRecalibrator --intermediate_csv_file inter.csv -I realigned.bam -R Homo_sapiens.GRCh37.68.dna.chromosome.all.fasta -o recal_data.grp --plot_pdf_file recal.pdf -knownSites dbsnp_137.b37.vcf -knownSites Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites 1000G_phase1.indels.b37.vcf --disable_indel_quals

This command has previously worked with other data using the same version of GATK.

Best Answer

Answers

Sign In or Register to comment.