Error 2: Files that had its sequence extracted: 0

Did you try running BiG-SCAPE previously with the same output folder? The main reason for not extracting sequences is that the program detects they are already there

As for error 1, I am not sure. Someone else had the same issue in another forum (https://github.com/nselem/bigscape-corason/issues/3) but we didn't get to the root of the cause.

Was it working before? How did you install it? Are you using the newest MIBiG reference (--mibig) or some of the older reference (--mibig14 or --mibig13)? Perhaps I'd suggest starting with the recommendations from the other post first (i.e. remove the "MIBiG_2.1.final" folder, use a different output folder) and then perhaps reinstalling BiG-SCAPE (download the current snapshot https://github.com/medema-group/BiG-SCAPE/archive/refs/heads/master.zip and reinstall the conda environment)

from big-scape.

Thank you for your quick reply! I ran Big-SCAPE on a remote server and it turned out that the errors are related to the enviroment setup.

For error 1, I solved it by setting for the new UTF-8 terminal support in Lion.

Setting for the new UTF-8 terminal support in Lion

export LC_CTYPE=en_US.UTF-8
export LC_ALL=en_US.UTF-8

Setting for the new UTF-8 terminal support in Lion

LC_CTYPE=en_US.UTF-8
LC_ALL=en_US.UTF-8
Error 2 seems to be caused by using an outdated package. By running the latest package, I managed to get the result.

However, I have another question about the BiG-SCAPE result interpretation. I tried to visulize it in Cytoscape.
In the .network file, there are multiple parameters including raw distance, squared similarity, jaccard index, DSS index, adjacency index, raw DSS non-anchor. Which parameter should be used as the edge attribute?

from big-scape.

Great to hear that it's working now! And thanks for sharing the solution :)

Regarding the network files for Cytoscape, use the raw distance. The other columns are components that lead to that final value.

Cheers!

from big-scape.