Duplicated entries in intermediate BAM file

[hoelzer]

I just noticed another thing... when using the BWA and minimap2 implementation in CLEAN and looking into the intermediate map-to-remove file there are duplicated entries for the contigs, e.g.:

@sq SN:JAAXOB010000001.1 LN:470666
@sq SN:JAAXOB010000001.1_2 LN:470666

However,

JAAXOB010000001.1

is part of my seal reference FASTA. But there is no JAAXOB010000001.1_2

This causes problems when one wants to use the file downstream...

Where does this come from?