ERROR MESSAGE: Unknown file is malformed in DepthOfCoverage

Hi there,

I am using DepthOfCoverage to get the exome coverage of a target reference and getting this error.
ERROR MESSAGE: Unknown file is malformed: Could not parse location from line: chr1 11873 12227 NR_046018_exon_0_0_chr1_11874_f 0 +

My command line is

ava -Xmx64g -jar GenomeAnalysisTK.jar
-T DepthOfCoverage
-I bamfiles.list //A list of paths to bam files
-R ucsc.hg19.fa
-L clinical_exome_cod.bed.interval_list
-geneList:REFSEQ exonTrack.refSeq.chr121XYM.sort
-ct 10 -ct 20 -ct 40 -ct 80 -ct 100
-o bamfiles

I used AWK to modify the refseq file as from the instructions at https://www.broadinstitute.org/gatk/guide/article?id=1329 and this same command was working when I did to get gene coverage.

So, what am I doing wrong now?

Thanks