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