Hi,

I'm working on RNA-seq data and have aligned my reads to the assembled transcript using bwa-mem. When I tried to run Picard Tools (`SamFormatConverter.jar`), the SAM dictionary threw an exception 

    "Cannot add sequence that already exists in SAMSequenceDictionary".

I then checked for duplication in the SAM file header and sure enough, two entries were duplicated. How do I correct this? Commands used are given below:

    bwa index contigs.fa
    bwa mem contigs.fa reads_1.fq reads_2.fq >samFile.sam
    java -Xmx4g -jar SamFormatConverter.jar INPUT=samFile.sam OUTPUT=bamFile.bam

This is where I faced the error.

I checked for duplicates using: 

    samtools view -HS samFile.sam | sort | uniq -c

2 @SQ entries were present >1 times.

Any help would be appreciated, thanks!
The `@SQ` headers that bwa emits come directly from the reference sequences in the index you're mapping against.

So the likely explanation for your problem is that the same entries are duplicated in your `contigs.fa` file.  You can check by looking at the `>` headers in your fasta file:

    grep '>' contigs.fa | sort | uniq -c

(If there are header lines like `>foo blah` and `>foo blah blah` then these will lead to duplicate `@SQ SN:foo` SAM headers while not being shown as exact duplicate lines by that `uniq` command.  So you may have to be a little careful in interpreting the results of that command.)