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HaplotypeCaller says dict does not exist, but it does!
I am running HaplotypeCaller and getting the error:
ERROR MESSAGE: Fasta dict file /net/rcnfs02/srv/export/duraisingh_lab/share_root/data/Plasmodium_knowlesi/jva/PlasmoDB-26_PknowlesiH_Genome_02.dict for reference /net/rcnfs02/srv/export/duraisingh_lab/share_root/data/Plasmodium_knowlesi/jva/PlasmoDB-26_PknowlesiH_Genome_02.fasta does not exist
BUT... the dictionary DOES exist! I made it with CreateSequenceDictionary.jar and it looks OK.
The reference dict and fasta are symbolically linked to the working directory. I did some googling on this but no luck.