GATK depthofcoverage problem

[gary]

Hi

I am using GATK depthofcoverage to calculate my exome-seq data:

 nohup java -jar ~/GATK/GenomeAnalysisTK-1.3-23-g13905c0/GenomeAnalysisTK.jar \
-T DepthOfCoverage -o depthofcoverage_sample1 -I Sample_1.bam \
-ct 10 -ct 20 -ct 30 -R hg19.fa -geneList Genome_UCSC.refseq -omitBaseOutput &

But the output file depthofcoverage_sample1.sample_gene_summary is empty.

I thought it was because I didn't sort my refseq file, whose first few lines are as follow:

#bin    name    chrom   strand  txStart txEnd   cdsStart        cdsEnd  exonCount       exonStarts      exonEnds        score   name2   cdsStartStat    cdsEndStat      exonFrames
0       NM_032291       chr1    +       66999824        67210768        67000041        67208778        25      66999824,67091529,67098752,67101626,67105459,67108492,67109226,67126195,67133212,67136677,67137626,67138963,67142686,67145360,67147551,67154830,67155872,67161116,67184976,67194946,67199430,67205017,67206340,67206954,67208755,       67000051,67091593,67098777,67101698,67105516,67108547,67109402,67126207,67133224,67136702,67137678,67139049,67142779,67145435,67148052,67154958,67155999,67161176,67185088,67195102,67199563,67205220,67206405,67207119,67210768,       0       SGIP1   cmpl    cmpl    0,1,2,0,0,0,1,0,0,0,1,2,1,1,1,1,0,1,1,2,2,0,2,1,1,
1       NM_001080397    chr1    +       8384389 8404227 8384389 8404073 8       8384389,8385357,8385877,8390268,8395496,8397875,8399552,8403806,        8384786,8385450,8386102,8390996,8395650,8398052,8399758,8404227,        0       SLC45A1 cmpl    cmpl    0,1,1,1,0,1,1,0,

So I downloaded the GATK sortByRef.pl file and typed the following command:

 perl SortByRef.pl Genome_UCSC.refseq ~/ref/UCSC/hg19/hg19.fa.fai

then I got an error:

Can not open temporary file 1045: Too many open files at SortByRef.pl line 95, <$INPUT> line 1021.

What am I doing wrong?