a) GATK version used: 3.8-1

b) Exact GATK commands used

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=64

#SBATCH --ntasks-per-core=1

#SBATCH --time=240:00:00

#SBATCH --mem=300g

$JAVA $GATK \

    -T GenotypeGVCFs \

    -R $ref \

    -V `find $outdir -name HaplotypeCaller.g.vcf | xargs | sed 's/ / -V /g'` \

    -o $outdir/_calling/jointcalls.g.vcf \

    -nt 64 \

($GATK refers to GenomeAnalysisTK.jar in my own directory)

c) The error log:

When I started running the job, it was kinda of bizarre that GenotypeGVCFs started on 2% instead of 0%. At the time the estimated running time is only 20h, which seemed normal to me as I was expecting finishing the job in less than a day using the multithreading option -nt 64:

INFO  17:24:48,596 ProgressMeter -   chr1:63136701         0.0    24.9 m    2474.2 w        2.0%    20.4 h      20.0 h

However, after 20+h of running, the joint calling is still on chr1 and the estimated finish time kept increasing and increased to 5.8w: 

INFO  13:27:35,331 ProgressMeter -   chr1:63582801         0.0    20.5 h   15250.3 w        2.1%     5.9 w       5.8 w 

Would appreciate if someone can let me know what went wrong. My colleague who used the same method didn't run into such a problem.