Could it be that you are using Java 1.7?
Picard used to run on Java 1.6 only.
From the Website:
The Picard command-line tools are packaged as executable jar files. They
require Java 1.6. They can be invoked as follows:
Best
John
On 08 Oct 2014, at 9:49 38am, Konstantinos Mavrommatis
<[email protected]> wrote:
> Hi,
> When I run CollectAlignmentMetrics and CollectInsertSizeMetrics using the
> latest Picard 1.119 I get the following error message.
> The same command line when run on a previous version of Picard (tried 1.107
> and 1.96) runs without issues and produces output.
> The BAM file was generated using STAR and was sorted using Picard SortSam.
> Thanks in advance for your help
> K
>
> Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch/RED/tmp/
> [Wed Oct 08 00:15:12 PDT 2014] picard.analysis.CollectInsertSizeMetrics
> HISTOGRAM_FILE=/gpfs/scratch/RED/tmp/InsertSize/3966/gpfs/archive/RED/RNA-Seq/Processed/STARaln.human-bamQC-SortByCo
> ordinates/InsertSize/O2_5.InsertSize.pdf
> METRIC_ACCUMULATION_LEVEL=[ALL_READS]
> INPUT=/gpfs/scratch/RED/tmp/InsertSize/3966/gpfs/archive/RED/RNA-Seq/Processed/STARaln.human-bamfiles-SortByC
> oordinates/O2_5.coord.bam
> OUTPUT=/gpfs/scratch/RED/tmp/InsertSize/3966/gpfs/archive/RED/RNA-Seq/Processed/STARaln.human-bamQC-SortByCoordinates/InsertSize/O2_5.InsertSize.qcstats
> REFERENCE
> _SEQUENCE=/gpfs/scratch/RED/tmp/InsertSize/3966/gpfs/reference/v1/Homo-sapiens/GRCh37.p12/WholeGenome/genome.fa
> TMP_DIR=[/scratch/RED/tmp/InsertSize/3966] VERBOSITY=WARN
> ING VALIDATION_STRINGENCY=SILENT DEVIATIONS=10.0 MINIMUM_PCT=0.05
> ASSUME_SORTED=true STOP_AFTER=0 QUIET=false COMPRESSION_LEVEL=5
> MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
> [Wed Oct 08 00:15:12 PDT 2014] Executing as @ussdgsphpccmp06 on Linux
> 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01;
> Picard version: 1.119(d44cdb51745f5e8075c826430a39d8
> a61f1dd832_1408991805) IntelDeflater
> [Wed Oct 08 00:15:12 PDT 2014] picard.analysis.CollectInsertSizeMetrics done.
> Elapsed time: 0.00 minutes.
> Runtime.totalMemory()=2026373120
> To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
> Exception in thread "main" java.lang.NullPointerException
> at
> htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:87)
> at
> picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:113)
> at
> picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53)
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
> at
> picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:124)
> at
> picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:83)
> child process exited with value 1
>
>
> Konstantinos Mavrommatis, PhD
> Senior Bioinformatics Scientist,
> Celgene Corp, San Francisco
> +1 415 839 7061
>
> *********************************************************
> THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS
> CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED
> INFORMATION INTENDED ONLY FOR THE USE OF THE INDIVIDUAL
> OR INDIVIDUALS NAMED ABOVE.
> If the reader is not the intended recipient, or the
> employee or agent responsible to deliver it to the
> intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this
> communication is strictly prohibited. If you have
> received this communication in error, please reply to the
> sender to notify us of the error and delete the original
> message. Thank You.
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk_______________________________________________
> Samtools-help mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/samtools-help
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
