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  • We encountered a non-standard non-IUPAC base in the provided reference '88'

    Hi,
    Currently, I am working with bowtie2 and GATK to call SNPs on sugarcane. I am using Sbicolor_v2.1_255.fa, sorghum genome downloaded from phytozome, as reference.
    java -Xms128m -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R Sbicolor_v2.1_255.fa -I input.sorted.bam -ploidy 8 -o input_gatk.vcf
    I run into the following error.
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
    ##### ERROR
    ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
    ##### ERROR The error message below tells you what is the problem.
    ##### ERROR
    ##### ERROR If the problem is an invalid argument, please check the online documentation guide
    ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ##### ERROR
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ##### ERROR
    ##### ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '88'
    ##### ERROR ------------------------------------------------------------------------------------------

    I hope someone can help me with these issues.
    Thanks in advance.

  • #2
    See : http://gatkforums.broadinstitute.org...d-reference-13

    The file from ftp://ftp.jgi-psf.org/pub/compgen/ph...v2.1_255.fa.gz

    appears to have "X"s in them ...

    grep -n "X" Sbicolor_v2.1_255.fa
    1653513:AGCCTCCCGTCCCCGATGTCTCCGACCACTGGTTAATATTCTTTXXXXXXXXXXXXXXXXXXXXXXXXXXCGGCGCTGGG
    5189698:TCAATAATTTATCACTAAATCCTTTXXXXXXXXXXXXXXXXXXXXXAAATGTTATCATGTCTCAAAACGTCTGATGAATG
    8205175:CTGTGTAGATAAGAXXXXXXXXXXXXXXXXXXXXXXXXXXCAAACAGGAAAGAGCGGCAGTGATTCAAGCAAAAACAAGT

    IUPAC codes are here: https://en.wikipedia.org/wiki/Nucleic_acid_notation

    I don't see X
    Last edited by Richard Finney; 08-27-2014, 02:52 PM.

    Comment


    • #3
      Apparently, the X means the sequence is masked for some reason, such as it was identified to be artificial (like vector sequence) and should not be in the assembly. I suggest you replace them with N.

      Comment


      • #4
        Thank you the reply. It is quite helpful.

        Comment

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