Hi
I am using GATK depthofcoverage to calculate my exome-seq data:
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:
So I downloaded the GATK sortByRef.pl file and typed the following command:
then I got an error:
What am I doing wrong?
I am using GATK depthofcoverage to calculate my exome-seq data:
Code:
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 &
I thought it was because I didn't sort my refseq file, whose first few lines are as follow:
Code:
#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,
Code:
perl SortByRef.pl Genome_UCSC.refseq ~/ref/UCSC/hg19/hg19.fa.fai
Code:
Can not open temporary file 1045: Too many open files at SortByRef.pl line 95, <$INPUT> line 1021.