Could you try downloading the latest version here:
http://broadinstitute.github.io/picard
Furthermore, I would recommend using java 1.6 or later,
N
On Tue, Dec 2, 2014 at 12:51 AM, L Rutter <lrutter0...@gmail.com> wrote:
> 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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