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


I got this error today running BaseRecalibrator:

ERROR stack trace

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


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