picard CreateSequenceDictionary complains about a contig being defined 2x

Question

[modockesner]

Here is the call

java -jar /source/picard-tools-1.102/picard-tools-1.102/CreateSequenceDictionary.jar REFERENCE=mm_ref.fa OUTPUT=mm_ref.dict

Error:

java -jar /source/picard-tools-1.84/picard-tools-1.84/CreateSequenceDictionary.jar REFERENCE=${PWD}/mm_ref.fa OUTPUT=${PWD}/mm_ref.dict
[Mon Jan 11 17:36:29 EST 2016] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/data/leelab/projects/common/mtrDmm10/mm_ref.fa OUTPUT=/data/leelab/projects/common/mtrDmm10/mm_ref.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 Jan 11 17:36:29 EST 2016] Executing as [e-mail] on Linux 2.6.32-431.29.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.84(1332)
[Mon Jan 11 17:36:29 EST 2016] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=514850816
FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" net.sf.picard.PicardException: Contig 'rDNA' already exists in fasta index.
    at net.sf.picard.reference.FastaSequenceIndex.add(FastaSequenceIndex.java:70)
    at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:142)
    at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
    at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
    at net.sf.picard.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:75)
    at net.sf.picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:132)
    at net.sf.picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:117)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    at net.sf.picard.sam.CreateSequenceDictionary.main(CreateSequenceDictionary.java:93)

I don't see a contig 2x

bak22@eris1n3 mtrDmm10]$ cat mm_ref.fa | awk '$1 ~ ">"{print $0}'
>chr1
>chr10
>chr11
>chr12
>chr13
>chr14
>chr15
>chr16
>chr17
>chr18
>chr19
>chr2
>chr3
>chr4
>chr5
>chr6
>chr7
>chr8
>chr9
>chrX
>chrY
>mtDNA
>rDNA
>GL456210.1
>GL456211.1
>GL456212.1
>GL456213.1
>GL456216.1
>GL456219.1
>GL456221.1
>GL456233.1
>GL456239.1
>GL456350.1
>GL456354.1
>GL456359.1
>GL456360.1
>GL456366.1
>GL456367.1
>GL456368.1
>GL456370.1
>GL456372.1
>GL456378.1
>GL456379.1
>GL456381.1
>GL456382.1
>GL456383.1
>GL456385.1
>GL456387.1
>GL456389.1
>GL456390.1
>GL456392.1
>GL456393.1
>GL456394.1
>GL456396.1
>JH584292.1
>JH584293.1
>JH584294.1
>JH584295.1
>JH584296.1
>JH584297.1

Newer versions give same result(1,102)

[Brice Sarver]

You are grepping the fasta file, but what about the fasta index itself? The error states:

Contig 'rDNA' already exists in fasta index.​

Perhaps try re-indexing your reference?

[modockesner]

Yes you are correct. rDNA was in the mm_ref.fai 2x. Not sure how. Removing one fixed this problem.

Thanks so much!