And on the point about not having a CreateSequenceDictionary jar, not too long ago Picard has changed to be a single command line jar and the first argument to that jar is the program you want to run.
On Tue, Dec 2, 2014 at 12:04 PM, Nils Homer <nho...@broadinstitute.org> wrote: > 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 >> >> >> >> ------------------------------------------------------------------------------ >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> >> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk >> _______________________________________________ >> Samtools-help mailing list >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help >> > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! 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