snakemake error: when timed out and snakemake became locked- Resolved

[nalbright]

Tried to run post pre trim workflow ($snakemake -p –use-singularity --configfile=config/custom_readfilt_workflow.json read_filtering_posttrim_workflow) but process timed out (computer died), then when try to attempt again I receive error: Error: snakemake -p --use-singularity --configfile=config/custom_readfilt_workflow.json read_filtering_posttrim_workflow Building DAG of jobs… Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:/home/user/dahak_2018/dahak/workflows If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

Resolved:

• $ snakemake --unlock

• deleted content in data directory

• $ export SINGULARITY_BINDPATH="data:/data"

• snakemake -p --use-singularity --configfile=config/custom_readfilt_workflow.json read_filtering_pretrim_workflow read_filtering_posttrim_workflow

[brooksph]

Great catch @nalbright! We’ll make sure to include this in docs. Keep making issues as you run in to stuff like this because even we’re aware we might forget to document it.

[charlesreid1]

Resolved by adding this information to a troubleshooting page in commit f4750b592252b30f5d4735ffed8bbbe0c5ee355f on the comparison-docs branch