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
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>> >> Samtools-help@lists.sourceforge.net
>> >> https://lists.sourceforge.net/lists/listinfo/samtools-help
>> >>
>> >
>> >
>> >
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>>
>
>
>
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--
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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