Hi ... Can you show explicitly what it lists when it lists the available programs? Also, why are you expanding the jar files?
I just downloaded the zip file from https://github.com/broadinstitute/picard/releases, unzipped it, went into the picard-tools-1.126 directory and ran your command (java -jar picard.jar CreateSequenceDictionary R=./Slal.Release.1.1.fasta O=./Slal.Release.1.1.dict) and it worked fine, except for the fact that I obviously don't have those files. -J On Wed, Dec 3, 2014 at 10:46 AM, L Rutter <lrutter0...@gmail.com> wrote: > Thank you for the syntax. > > > 1) I must be doing something wrong, because when I run: > > java -jar picard.jar CreateSequenceDictionary R=./Slal.Release.1.1.fasta > O=./Slal.Release.1.1.dict > > I receive the message: > > USAGE: PicardCommandLine <program name> [-h] > > Available Programs: > -------------------------------------------------------------------------------------- > > 'CreateSequenceDictionary' is not a valid command. See PicardCommandLine > --help for more information. > > > 2) And, when I run: > > java -jar picard.jar > > I receive the message: > > USAGE: PicardCommandLine <program name> [-h] > > Available Programs: > -------------------------------------------------------------------------------------- > > > 3) I am not sure if I am missing a step, but what I did was: > - I downloaded the file picard-tools-1.126.zip > - unzip picard-tools-1.126.zip > - jar -xvf htsjdk-1.126.jar > - jar -xvf picard.jar > - jar -xvf picard-lib.jar > > > Thanking you again for any advice... > L. Rutter > > On Tue, Dec 2, 2014 at 8:10 PM, George Grant <ggr...@broadinstitute.org> > wrote: >> >> If you download picard-tools.1.126.zip from github: >> (https://github.com/broadinstitute/picard/releases/tag/1.126) and unpack it, >> you can then execute the picard jar itself to run the command that used to >> be packaged separately. >> >> So try: >> java -jar picard.jar CreateSequenceDictionary R=./Slal.Release.1.1.fasta >> O=./Slal.Release.1.1.dict >> >> (and if you just execute "java -jar picard.jar" it will give you a >> comprehensive list of the tools that are available) >> >> George >> >> On Tue, Dec 2, 2014 at 9:04 PM, L Rutter <lrutter0...@gmail.com> wrote: >>> >>> Thank you both for your help! >>> >>> I did download picard-tools 1.126, but am unsure how to run the command. >>> I believe this is what Jeff was trying to describe to me, but I miss be >>> missing something. When I click on your link, it redirects to this website >>> (http://www.actuate.com/info/sf-eds-nl-f-type-download/), and I am not sure >>> how that is related. >>> >>> In any case, I tried running this: >>> >>> java -jar picard-tools/1.126/CreateSequenceDictionary.jar >>> R=./Slal.Release.1.1.fasta O=./Slal.Release.1.1.dict >>> >>> >>> Unsurprisingly, I received this error: >>> >>> Failed to load Main-Class manifest attribute from >>> picard-tools/1.126/CreateSequenceDictionary.jar >>> >>> >>> I looked inside the picard-tools folder, and there are four files >>> (htsjdk-1.126.jar libIntelDeflater.so picard.jar picard-lib.jar). Only >>> two of them seem to mention CreateSequenceDictionary in them: >>> >>> >>> picard/sam/CreateSequenceDictionary.class in picard-lib.jar >>> >>> picard/sam/CreateSequenceDictionary.class in picard.jar >>> >>> >>> I am unsure how to form the syntax to create the .dict file from my >>> .fasta file. >>> >>> >>> Thank you again for any advice. >>> >>> >>> L. Rutter >>> >>> >>> >>> On Tue, Dec 2, 2014 at 1:31 PM, Jeff Gentry <jgen...@broadinstitute.org> >>> wrote: >>>> >>>> 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! 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 >>> >> >> >> >> -- >> George B. Grant >> GP Informatics >> Broad Institute of MIT and Harvard >> 75 Ames St, 7003FF >> Cambridge, MA 02141 >> Phone: 617-714-7656 >> > ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! 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