The bioBakery help forum

Rerun, locked and frozen

Hi,

I can to cancel my bioBakery workflow and restart but I got an error saying that I cannot proceed because there is a lock. How do I unlock? Sorry, I lost the error message. When I try to remove the directory I get the following error message:

rm: cannot remove ‘test/.nfs0000000385330c0a00000027’: Device or resource busy

Also, do I have to add any parameters to the code to prevent it from rerunning completed tasks?

Running the whole analysis to a different directory prevented the error message from appearing but now nothing is happening when I run the code, its just frozen, there is no output, and I cannot exit the code using ctl-C. It freezes if when I run biobakery_workflows --help I tried deleting the condo environment but I many errors all saying that it connot remove or renmae certain files. Here is an example of one of the errors:

WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(140): Could not remove or rename /home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/numpy/random/.nfs00000003846eac0400000059. Please remove this file manually (you may need to reboot to free file handles)

I installed bioBakery using Conda on my Linux machine with a slurm grid. My code:

biobakery_workflows wmgx \
--input data/ \
--output directory/ \
--grid slurm \
--grid-jobs 6 \
--grid-partition Research \
--threads 8

Best,
Ali