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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