GATK file lock error while using VariantRecalibrator

[karl_s]

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

[lindenb]

check that GATK can write in the folder: /mnt/gnas1/Analysis/IbrutinibResistance/WEX/GATK/CLL/200-013-3_20_13_L7.LB2/

[karl_s]

Yes, I think it can. I have been writing all of the other data into this same directory and the other GATK codes dont have this problem. just to be sure I went and chmod 755 all the directories.

I just reran the variant caller with the UnifiedGenotyper and tried to validate the vcf with ValidateVariants and I got the same error.

[karl_s]

OK so here is something interesting. When I copy the vcf file and index to another directory on the local machine it works. For the analses, I have been using a fileserver, and remotely mounting the share on my linux machine. I think the filserver is a windows machine exporting NFS. Maybe there is some bizzare effect caused by this. Maybe someone else has had this problem, since its not an unusual configuration.

[greekkey]

Hi, karl_s. I'm now encountered the same problem. I am analyzing exome data using GATK 3.8. The data was stored on a NAS connect with my computer via LAN.
For the steps of bam file callibration (-T RealignerTargetCreator / -T IndelRealigner / -T BaseRecalibrator / -T PrintReads) and gvcf extraction (-T HaplotypeCaller), it worked well. But when I entered the step of generation vcf file from gvcf file (using -T GenotypeGVCFs), I got a similar "ERROR MESSAGE: An error occurred while releasing the lock for file /mnt/nas/filename.g.vcf.idx". Exactly the same as your experience, when I download the gvcf files to local disk, and using the ref database in my local disk, my commend went on well.

Did you solved that problem since your last post?