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  • Problems Running Picard's ReorderSam

    Hello everyone,

    I've been trying to use Picrad's ReorderSam.jar tool to sort one BAM file, because I want to use it later with GATK. But, every time that I try to sort the file I get the following error:

    "2011-09-07 00:02:48 ReorderSam No reference sequence dictionary found. Aborting. You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.
    [Wed Sep 07 00:02:48 GMT 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
    Runtime.totalMemory()=1012269056"

    I have already created a dictionary as requested using CreateSequenceDictionary.jar and stored it on the same folder as the reference.

    However, despite I have created the dictionary, I keep getting the same error message.

    The commands that I used to call the run the .jar files are:

    CreateSequenceDictionary.jar
    "/usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/CreateSequenceDictionary.jar R= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa O= GRCh37_hg19_masked.fa.bai"


    ReorderSam.jar
    " /usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/ReorderSam.jar I= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_sorted.bam O= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_GATK_sorted.bam REFERENCE= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa"


    Also, I have already tried with different extension suffixes for CreateSequenceDictionary.jar output file and I have already verified that my BAMfile has headers (i.e. @SQ SN:gi|224589801|ref|NC_000010.10| LN:135534747 lines)

    Thank you very much!!

    Martin

  • #2
    In case someone else had this problem I found the solution here:



    Cheers,
    Martin

    Comment


    • #3
      Thank you for posting the solution when you found it, Martin! I wish everyone would do this. You are the fairy godcoder of the internet.

      Comment


      • #4
        Originally posted by Artur Jaroszewicz View Post
        Thank you for posting the solution when you found it, Martin! I wish everyone would do this. You are the fairy godcoder of the internet.

        No worries, I think is better to share the info and save the painstaking process of finding the solution to others... (if I already found one…) The solution here was to name the dictionary with the “.dict” extension as stated on the link.

        Cheers Artur!

        Comment

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