Runing canu in conda environment in HPC, which one is the assembly contig file I that I should get?
Closed this issue · 3 comments
JWang52md commented
skoren commented
I suspect it's running on the grid (https://canu.readthedocs.io/en/latest/faq.html#how-do-i-run-canu-on-my-slurm-sge-pbs-lsf-torque-system), what was the output of the command you ran? If it says submitted that is the case, you can turn off grid use with useGrid=false
.
alpapan commented
@JWang52md when you run canu on a grid, without the use grid set to false, canu's command submits the scripts to the grid and then exits.
Assuming you submitted them correctly, you should check the job queue and wait for your jobs to finish.
skoren commented
Idle, answered above