Badly formed genome loc
Trying to run diagnoseTargets with a list of genes as intervals: java -jar GenomeAnalysisTK.jar -T DiagnoseTargets -R Final.HMP.fasta -o genes.output.new.vcf -I bam.list -L gene.intervals.list
ERROR MESSAGE: Badly formed genome loc: Contig '@SQ SN:lcl|NZ_ABYJ02000001.1 LN' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
However, this sequence exists in the dictionary:
grep "lcl|NZ_ABYJ02000001.1" Final.HMP.dict
@SQ SN:lcl|NZ_ABYJ02000001.1 LN:27533 UR:file:/seq/msctmp/moran/RISK/HMP.katz/Final.HMP.fasta M5:a492998ddf8c8b4f9d6aad4d7d4c26d5
And in the header of the interval files:
grep "lcl|NZ_ABYJ02000001.1" ../Raw/HMP649/gene.intervals.list
@SQ SN:lcl|NZ_ABYJ02000001.1 LN:27533
I'm sorry, but have been working on this for hours, can't figure it out.