Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
To run the programming "GenotypeGVCFs" too slow for my data, why??
SAMPLE=" -V d_19_HC.gvcf -V d_F14_HC.gvcf -V d_F8_HC.gvcf -V d_M12_HC.gvcf -V d_M5_HC.gvcf -V d_X4_HC.gvcf -V d_X9_HC.gvcf "
java -Xmx8g -jar $GATK -T GenotypeGVCFs -R $GENOME -nt 32 $SAMPLE -o gvcf_vcf_test1.vcf -L CI01000059 >gvcf_vcf_test1.log 2>&1
There exists some records in my file.log as the below:
WARN 01:12:58,923 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /lustre/home/xqxia/yxchen/HC_gvcf/gvcf_vcf/d_19_HC.gvcf.idx because an IOException occurred with message: Function not implemented.
INFO 01:12:58,925 RMDTrackBuilder - Could not acquire a shared lock on index file /lustre/home/xqxia/yxchen/HC_gvcf/gvcf_vcf/d_19_HC.gvcf.idx, falling back to using an in-memory index for this GATK run.
WARN 02:46:50,988 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /lustre/home/xqxia/yxchen/HC_gvcf/gvcf_vcf/d_F14_HC.gvcf.idx because an IOException occurred with message: Function not implemented.
I use 3.6 version GATK.