Frequently Asked Questions

If you have more question please write us a ticket on github.

MPRAsnakeflow is not able to create a Conda environment

If you get a message like:

Caused by: json.decoder.JSONDecodeError: Extra data: line 1 column 2785 (char 2784)#

Try to do the following steps

rm -r .snakemake/metadata .snakemake/incomplete

Afterwards try MPRAsnakeflow again. If the above error still occurs, rerun after deleting the entire .snakemake folder.

Can I use STARR-seq with MPRAsnakeflow?

No, not yet!

The pipeline is giving an error “BUG: Out of jobs ready to be started, but not all files built yet.” and won’t run. How can I fix this?

Please update snakemake, as this error is highly likely to have occured from snakemake internal issues.