Hi there ... I'm stumped. Are you still using Java 1.5? If so, can you try using 1.6 or later and see if that helps?
When I unzip that zip file, the files are ending up in a subdirectory, picard-tools-1.126 and not in the current directory. Is it possible that perhaps you're still pointing at the wrong picard.jar? That seems unlikely as the one you have does seem to be the single command line version. Just to double check, what happens if you run this command? unzip -t picard.jar | grep CreateSequenceDictionary -J On Wed, Dec 3, 2014 at 3:13 PM, L Rutter <lrutter0...@gmail.com> wrote: > Hello all: > > I really appreciate your patience. > > 1) I re-downloaded the picard-tools-1.126.zip file from the website you > mentioned. > > 2) I ran the following command: unzip picard-tools-1.126.zip. > > 3) This led me to have the following 6 items, all in the same folder: > - htsjdk-1.126.jar > - libIntelDeflater.so > - picard.jar > - picard-lib.jar > - Slal.Release.1.1.fasta > - Slal.Release.1.1.fasta.fai > > 4) I ran the commmand: > java -jar ./picard.jar CreateSequenceDictionary R=./Slal.Release.1.1.fasta > O=./Slal.Release.1.1.dict > > And this was the entire output: > > USAGE: PicardCommandLine <program name> [-h] > > Available Programs: > -------------------------------------------------------------------------------------- > > 'CreateSequenceDictionary' is not a valid command. See PicardCommandLine > --help for more information. > > 5) I ran the command: java -jar picard.jar > > And this was the entire output: > > USAGE: PicardCommandLine <program name> [-h] > > Available Programs: > -------------------------------------------------------------------------------------- > > > 6) This is all that I did, so if I need to run any additional commands > besides unzip on the downloaded zip file, then I have not done that. The > outputs are entire - they do not list any available programs! > > Thanking you… > L. Rutter > > On Wed, Dec 3, 2014 at 10:22 AM, Jeff Gentry <jgen...@broadinstitute.org> > wrote: >> >> 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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