Did you try running this using Java 1.6 or later? I would be hesitant to
support 1.5 or earlier, and we are discussing requiring 1.7 or later moving
forward,
N
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
>> >>
>> >
>>
>
>
>
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>
>
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