Error in running GenomicsDBConfigException

Question

[shivangi.agarwal800]

Hi Guys,

I am running GATK for variant calling using bam files for two samples (example). I first created gvcf using following commands:

java -jar $GenomeAnalysisTK HaplotypeCaller -R hg19-agilent.fasta -I aln_501_trimmed_again_RG.bam -O aln_501_trimmed_again_RG.g.vcf -ERC GVCF

java -jar $GenomeAnalysisTK HaplotypeCaller -R hg19-agilent.fasta -I aln_502_trimmed_again_RG.bam -O aln_502_trimmed_again_RG.g.vcf -ERC GVCF

Then, I am trying containing database (in external drive which is 28 TB) as below: java -jar $GenomeAnalysisTK GenomicsDBImport -V aln_501_trimmed_again_RG.g.vcf -V aln_502_trimmed_again_RG.g.vcf --genomicsdb-workspace-path my_database --intervals chr1.bed.

But getting error as :

terminate called after throwing an instance of 'GenomicsDBConfigException' what(): GenomicsDBConfigException : Syntax error in JSON file /tmp/loader_11705777375230343382.json Aborted (core dumped)

Also, I am getting a pop up in my system as "low disk space in Filesystem root"

Is this error due to disk space or something else? How much disk space do I need for running this command? I am running these analysis in additional storage drives which are 28 TB. Please suggest.

[shivangi.agarwal800]

Hi,

Can anyone please suggest on the above query? I will highly appreciate your suggestions.

[Pierre Lindenbaum]

ask the GATK help forum https://gatk.broadinstitute.org/hc/en-us/community/topics