Hi, I am having some problems with the GATK pipeline. I followed the instructions on the GATK website to preprocess a fastq file, and this worked fine. Then moving on to variant discovery using the HaplotypeCaller, i get a vcf file and thats fine. When I try to use the VairantRecalibrator, I get an error that I think others have seen:
##### ERROR MESSAGE: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file /mnt/gnas1/Analysis/IbrutinibResistance/WEX/GATK/CLL/200-013-3_20_13_L7.LB2/raw_variants_vcftools.recode.vcf.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system.
I tried rebuilding the vcf using vcftools, and I get the same error. I am running RHEL6. Any ideas?
Thanks much,
karl
##### ERROR MESSAGE: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file /mnt/gnas1/Analysis/IbrutinibResistance/WEX/GATK/CLL/200-013-3_20_13_L7.LB2/raw_variants_vcftools.recode.vcf.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system.
I tried rebuilding the vcf using vcftools, and I get the same error. I am running RHEL6. Any ideas?
Thanks much,
karl
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