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
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>>> >
>>> >
>>> >
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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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