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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(
at java.util.concurrent.locks.ReentrantLock$FairSync.tryAcquire(
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireInterruptibly(
at java.util.concurrent.locks.ReentrantLock.lockInterruptibly(
at java.util.concurrent.PriorityBlockingQueue.take(
at org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceAsMuchAsPossible(
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$
at java.util.concurrent.Executors$
at java.util.concurrent.FutureTask$Sync.innerRun(
at java.util.concurrent.ThreadPoolExecutor.runWorker(
at java.util.concurrent.ThreadPoolExecutor$

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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