Robert Chase

Did you have separate environments for rosetta and folding or did you install the folding.yml into the PyRosetta env?

This line of the run_pyrosetta_ver.sh script sources the pyrosetta environment, not the folding environment. https://github.com/RosettaCommons/RoseTTAFold/blob/main/run_pyrosetta_ver.sh#L30 The README says, "The latter is required to run a pyrosetta version only". I think...

duplicate of #68

I am having a similar issue on gridengine.

When I run this command: bcbio_nextgen.py ../config/sampleconfig.yaml -t ipython -n 5 -s sge -q linux01.q -r conmem=12 I get this error message: The cluster startup timed out. This could be...

It says 0 engines running so it looks like it's pending? I'll add a longer timeout with the --timeout flag.

-bash-3.2$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 159 0.60000 bcbio-e rerpc dr 03/08/2018 16:29:20 5 1 253 0.50000 bcbio-c rerpc r 03/08/2018 16:35:20 1...