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Badly formed genome loc
I've been trying to figure out the source of the following error message in the past few days but got nowhere:
Command: java -Xmx4g -jar gatk/GenomeAnalysisTK.jar -R /mnt/blac1/ratRefGenome/rn5.gatk.fa -I /mnt/blac1/rn5.fixed.bam -T IndelRealigner -targetIntervals /mnt/blac1/realign.intervals -o /mnt/blac1/realigned.bam
ERROR MESSAGE: Badly formed genome loc: Contig chrX_JH620458_random given as location, but this contig isn't present in the Fasta sequence dictionary
gatk version: GenomeAnalysisTK-2.3-9-ge5ebf34
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)
Linux wkst 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
I've checked and found chrX_JH620458_random in the rn5.gatk.fa file. I've deleted the .dict file and .fai file and got the same error. chrX_JH620458_random is not in realign.intervals but is the last contig in the rn5.gatk.fa file.
Your advise is very appreciated!
Univ. Tennessee Health Sci Ctr.