The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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.