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  • Cannot add sequence that already exists in SAMSequenceDictionary

    I am just learning how to analyse data

    this is my steps

    1. download library, combine them into single csv file by CRISPR.sgRNA_create_ref_fasta

    2. bowtie2 apple$ ./bowtie2-build CL.fa CrL

    3.Billyde-MacBook:bowtie2 apple$ ./bowtie2 -x CrL -U -f R.fa -S


    4Picard Sortsam
    -> apple$ java -Xmx2g -jar picard.jar SortSam INPUT=test OUTPUT=result.sam SORT_ORDER=queryname

    but error-> Cannot add sequence that already exists in SAMSequenceDictionary: A1BG


    - - -
    with:
    ./samtools view -H R
    [W::sam_hdr_parse] duplicated sequence 'A1BG'
    [W::sam_hdr_parse] duplicated sequence 'A1BG'
    [W::sam_hdr_parse] duplicated sequence 'A1CF'
    [W::sam_hdr_parse] duplicated sequence 'A1CF'
    [W::sam_hdr_parse] duplicated sequence 'A2M'
    [W::sam_hdr_parse] duplicated sequence 'A2M'
    [W::sam_hdr_parse] duplicated sequence 'A2ML1'
    [W::sam_hdr_parse] duplicated sequence 'A2ML1'
    [W::sam_hdr_parse] duplicated sequence 'A3GALT2'
    [W::sam_hdr_parse] duplicated sequence 'A3GALT2'
    ... and many


    - -

    do there have any idea why " Cannot add sequence that already exists in SAMSequenceDictionary: A1BG"

    I have tried many different way to fit it but still not work

    I have also try
    samtools rmdup <input.bam> <output.bam>
    or
    samtools rmdup -s <input.bam> <output.bam>

    butnotthing help



    -

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