Hi, I have a problem in that PICARD MarkDuplicates appears to error near the end of its process -- with a temp file not found error.

This is running in a GATK pipeline on our cluster for WGS Best Practices.

Error is;
Exception in thread "main" java.lang.IllegalStateException: Non-zero numRecords but /tmp/rwillia/CSPI.7224120933399878689.tmp/2.tmp does not exist

We get the same error with picard 2.9.2 and picard 2.0.1 . The java being used is:
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)

We have tried multiple different BAM files as tests and get the same error.

Has anybody else seen this "tmp does not exist error" before? Was there a fix that worked?I cannot see this error previously reported.
I can run MarkDuplicates using a standalone Qsub tester script and I get the same error.

I made the directory /tmp/rwillia on the scratch drive but it did not help.
Thanks for any help,
Cheers,
Roy Williams

Test qsub script

PBS -l walltime=99:00:00

PBS -l nodes=1:ppn=8:memory=29gb

export TMPDIR=/scratch/rwillia
module load samtools
module load picard
java -Xmx26g -jar /opt/applications/picard/2.1.0/bin/picard.jar MarkDuplicates \
I=/mnt/loring/data/OMICS_PIPE_DATA/ANALYSIS/DNAseq/RW_WGS/BWA_RESULTS/REACH000450/REACH000450_sorted.rg.bam \
O=/mnt/loring/data/OMICS_PIPE_DATA/ANALYSIS/DNAseq/RW_WGS/BWA_RESULTS/REACH000450/REACH000450_sorted.rg.md.bam \
M=/mnt/loring/data/OMICS_PIPE_DATA/ANALYSIS/DNAseq/RW_WGS/BWA_RESULTS/REACH000450/REACH000450_sorted.rg.md.metrics.txt \
ASSUME_SORTED=true \
VALIDATION_STRINGENCY=LENIENT

picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 14.35 minutes.
Runtime.totalMemory()=21026570240
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: Non-zero numRecords but /tmp/rwillia/CSPI.7224120933399878689.tmp/2.tmp does not exist
at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:141)
at htsjdk.samtools.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:86)
at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.remove(DiskBasedReadEndsForMarkDuplicatesMap.java:61)
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:388)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:185)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Roy Williams, Ph.D.
Bioinformatics Director,
The Center for Regenerative Medicine,
Scripps Research Institute,
10550 North Torrey Pines Road
San Diego, California, 92121
USA