Hi starr,
This is likely because you ran out of space on disk drive for temporary
files. Try setting TMP_DIR= to a folder with some space.
Colin
On 19 June 2014 05:54, Hazard, E. Starr <haza...@musc.edu> wrote:
> 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
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
