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.
Having trouble running GenotypeGVCFs with around 50 samples
Hi. I may be making a simple mistake but I cannot figure out what is going on at all. I am currently trying to run GenotypeGVCFs on around 50 whole human genome samples. These samples were produced with haplotype caller. The interesting thing is earlier while I was waiting to finish calling of all my samples I ran it on some 20 samples with no problem. I may just be not allocating enough memory however it seems like GATK does not even begin to process the files. I am running on a LSF server in a docker container so I would normally think the problem could be on my end but it was running with some 20 samples. Should I have to Combinegvcfs because I am using whole genome sequences or possibly do you guys have a memory suggestion.
The only error I seem to get is this :
Traceback (most recent call last):
File "/opt/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin/docker_run.py", line 598, in
File "/opt/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin/docker_run.py", line 577, in main
ret = run_docker(argv)
File "/opt/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin/docker_run.py", line 526, in run_docker
docker_image = os.environ['LSB_DOCKER_IMAGE']
File "/usr/lib/python2.7/UserDict.py", line 23, in getitem
Yet it does run with a small sample size.