Hello:
Thanks again for your help.
It seems that when I use Java 1.8, then it works (but I did not try 1.6 or
1.7). That was the only thing I changed, I believe.
When I was using Java 1.5 or 1.8, and ran the command you asked (unzip -t
picard.jar | grep CreateSequenceDictionary), I got the following output:
testing: picard/sam/CreateSequenceDictionary.class OK
Thanks again!
L. Rutter
On Wed, Dec 3, 2014 at 2:53 PM, Nils Homer <nho...@broadinstitute.org>
wrote:
> 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
>>> >>> _______________________________________________
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>>> >>> 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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>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>>
>
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