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
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