I am currently trying to run the nextflow cutandrun pipeline on my Windows PC. I have successfully run this pipeline with a dataset from a published article, however I am getting an error when I try to run my own dataset shown below:
My dataset is larger than the test one I used, and I am wondering if this has anything to do with maxing out my available RAM. All help appreciated, I have a very rudimentary bioinformatics/cs background. Thank you!
The error indicates an issue with the output file.
Do you have enough disk space on your machine for the output to be written?
Thanks for your quick response. How much is typically recommended? I think I have ~15GB available in my SSD currently.
I can’t say. I don’t know how the intermediate files and outputs scale with inputs. It may be better to ask on the nf-core slack channel for #cutandrun where the pipeline maintainers should be more active.
The lazy solution is run it on cloud or linux server if you have access to those.
If you are limited by your machine, and you are familiar with downsampling, I would like to suggest running it with 50% (10%) of the reads.
You could monitor your ram/ CPU/ disk usage with the 50% or 10% of the downsampled run.
