Hello,
I am trying to create sequence dictionary of my .fasta file, using
picard-tools.
I downloaded picard-tools from (
http://sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip/download),
and saw that it did include CreateSequenceDictionary.jar.
Then, I ran the following command:
java -jar picard-tools/1.119/CreateSequenceDictionary.jar
R=./Slal.Release.1.1.fasta O=./Slal.Release.1.1.dict
I received the following output:
picard.sam.CreateSequenceDictionary REFERENCE=./Slal.Release.1.1.fasta
OUTPUT=./Slal.Release.1.1.dict TRUNCATE_NAMES_AT_WHITESPACE=true
NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Dec 01 23:36:53 CST 2014] Executing as lrut...@school.edu on Linux
2.6.32-279.19.1.el6.x86_64 x86_64; GNU libgcj 1.5.0; Picard version:
1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) IntelDeflater
[Mon Dec 01 23:36:53 CST 2014] picard.sam.CreateSequenceDictionary done.
Elapsed time: 0.00 minutes.
Runtime.totalMemory()=15572992
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at java.util.regex.Matcher.toMatchResult(libgcj.so.10)
at java.util.Scanner.myCoreNext(libgcj.so.10)
at java.util.Scanner.myFindPInStr(libgcj.so.10)
at java.util.Scanner.findInLine(libgcj.so.10)
at java.util.Scanner.findInLine(libgcj.so.10)
at
htsjdk.samtools.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:123)
at
htsjdk.samtools.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
at
htsjdk.samtools.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:92)
at
htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:75)
at
picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:136)
at
picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:121)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at
picard.sam.CreateSequenceDictionary.main(CreateSequenceDictionary.java:97)
The version of JVM that I am using is:
java version "1.5.0"
gij (GNU libgcj) version 4.4.7 20120313 (Red Hat 4.4.7-4)
I also tried to download the most recent version of picard-tools (
https://github.com/broadinstitute/picard/releases/download/1.126/picard-tools-1.126.zip),
but this did not contain a CreateSequenceDictionary.jar file.
Thanking you for any advice!
L. Rutter
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