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FASTA problem - RealignerTargetCreator
I am having problem to run the RealignerTargetCreator.
java -Xmx4g -jar /mit/sjlabrie/software/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \ -T RealignerTargetCreator \ -R $fasta \ -I alnSortedNoDupRG1.bam \ -o alnSortedNoDupRG1.intervals
Here is the error message:
ERROR MESSAGE: Invalid command line: Failed to load reference dictionary
When I create a dictionary with a Picard CreateSequenceDictionary it seems good:
@HD VN:1.4 SO:unsorted @SQ SN:m4-202 LN:37850 UR:file:/net/eaps-80-11/data/sjlabrie/m4-202_AAAA/m4_202_reaRev.gb.txt M5:c34f2bad5f5667604f34a26cd8baf86e
This file has a .txt extension. To make everything conform with my internal nomenclature, I renamed that file .fasta:
mv fl.txt fl.fasta
Then recreate a dict with CreateSequenceDictionary and here is the new dictionary:
@HD VN:1.4 SO:unsorted
This is really puzzling me and driving me somewhere I don't really want to go.
Thank you for your help,