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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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Temporary directory #935

Closed hanrong498 closed 1 year ago

hanrong498 commented 1 year ago

Hi,

I am trying to run WGBS pipeline and get the error mktemp: failed to create directory via template ‘/data/extended//snakepipes.XXXXXXXXXX’: No such file or directory I think this issue was also mentioned here

Reading the documentation, I wonder if it is possible that the tempDir needs to be set differently.

The HPC cluster in my university uses Linux system and /tmp/${SLURM_JOB_ID} for temporary files. Maybe I should change to tempDir = /tmp/?

Thanks!

hanrong498 commented 1 year ago

followup: yes changing it to tempDir = /tmp/does solve the problem