Folks,
When I run PicardTools on the head node of my cluster
java -Xmx22g -jar ${PICARDPATH}/SortSam.jar INPUT=/PATH/TO/my.bam
OUTPUT=/PATH/TO/my_sorted_QN.bam CREATE_INDEX=true
VALIDATION_STRINGENCY=STRICT SORT_ORDER=queryname
The sort process finishes.
However, when I run ( the same command) on a COMPUTE-NODE I see the following
…
INFO 2014-06-18 17:03:26 SortSam Read 60,000,000 records. Elapsed time:
00:08:49s. Time for last 10,000,000: 84s. Last read position:
chr5:80,110,210
[Wed Jun 18 17:03:30 EDT 2014] net.sf.picard.sam.SortSam done. Elapsed time:
8.89 minutes.
Runtime.totalMemory()=3817734144
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.samtools.util.RuntimeIOException:
java.io.IOException: No space left on device
The head node has 24G ram. The compute nodes also have 24G ram.
Head node:
java -version
java version "1.7.0_55"
OpenJDK Runtime Environment (rhel-2.4.7.1.el6_5-x86_64 u55-b13)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)
ssh compute014
compute014: java -version
java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (rhel-1.39.1.9.7.el6-x86_64)
OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode)
So clearly the JAVA did not get distributed to the compute nodes but is that
likely to be the problem? The crashing occurred prior to upgrading to JAVA 7
Any suggestions for trouble shooting this problem will be appreciated.
Thanks,
Starr
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