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GenomicsDBImport "RunConfigException" Error when scale is high
I am having a problem in successfully running
GenomicsDBImport with ~10K samples. Most of the times, I get this below mentioned error, while in a very few cases (genomic intervals) I had success.
terminate called after throwing an instance of 'RunConfigException' what(): RunConfigException : ifs.is_open()
Could you help me to understand the error message please ?
Note: I have a decent
ulimit set (~65K) , so higher number of file descriptors can open at the same time.
The code I run: GATK version: 22.214.171.124
java -d64 -Xmx64g -Xms64g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar gatk.126.96.36.199.jar GenomicsDBImport \ --genomicsdb-workspace-path /some/path/genomicsdb-workspace \ --interval-padding 500 \ --batch-size 50 \ --intervals chr1:257667-297968 \ --reader-threads 5 \ --TMP_DIR /some/path/tmp \ --variant /some/path/sample1.vcf.gz --variant /some/path/sample2.vcf.gz ....... --variant /some/path/sample10000.vcf.gz