Cannot add sequence that already exists in SAMSequenceDictionary

[Flyingfrog]

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


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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


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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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