Refseq file 0 coding length

Question

[whb]

Hi,

I would like to use gatk DepthOfCoverage to get coverage of each gene. I have created a refseq file according to gatk website from UCSC table browser. The first few lines of the refseq file are below but keep getting an error saying the coding length of some genes are 0. and the output gene coverage file is empty which looks like gatk cannot read the start and end of the exon??

gatk DepthOfCoverage \
-R mm10.fa \
-O 153DoC \
-I 153.bam \
-gene-list target.refseq \
-L ${bed}

Reseq file

> #bin  name    chrom   strand  txStart txEnd   cdsStart    cdsEnd  exonCount   exonStarts  exonEnds    score   name2   cdsStartStat    cdsEndStat  exonFrames
> 1082  NM_001111320    chr1    -   65158615    65186479    65159464    65175352    9   65158615,65161049,65161799,65165099,65166106,65168498,65170958,65175230,65186304,   65159555,65161212,65161940,65165251,65166284,65168604,65171250,65175368,65186479,   0   Idh1    cmpl    cmpl    2,1,1,2,1,0,2,0,-1,
> 222   NM_001136104    chr1    +   156558786   156649619   156559048   156642716   13  156558786,156620838,156622484,156625287,156629852,156631344,156633079,156633752,156635064,156636817,156640438,156640992,156641541,  156559205,156620901,156622655,156625583,156630125,156631429,156633257,156633937,156635217,156636907,156640612,156641229,156649619,  0   Abl2    cmpl    cmpl    0,1,1,1,0,0,1,2,1,1,1,1,1,

*

Error
17:15:33.131 WARN  Utils - **********************************************************************
17:15:33.132 WARN  Utils - * WARNING:
17:15:33.132 WARN  Utils - * 
17:15:33.132 WARN  Utils - * RefSeq file contains transcripts with zero coding length. Such
17:15:33.132 WARN  Utils - * transcripts will be ignored (this warning is printed only once)
17:15:33.132 WARN  Utils - **********************************************************************