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.