Gert Hulselmans

Try again. Probably github was temporarily down.

You need to have a C++ compiler installed (e.g. `g++`). It might be easier to install it via conda: https://daler.github.io/pybedtools/main.html

There might be a chance that one of the worker processes was crashed and that ray didn't detect it and assumes it is still running. Try with less cores or...

`http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes` seems accessible again.

Are you sure the filenames you made, exist? What is the output of: ```python # File exists? print(rankings_db, os.path.isfile(rankings_db)) print(scores_db, os.path.isfile(scores_db)) print(motif_annotation, os.path.isfile(motif_annotation)) ``` You can also change `/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/ctxcore/rnkdb.py` ```...

Your input file is very likely corrupt. I assume decompressing the file with gzip will fail too: ``` # Try to decompress the file. gzip -cd fragments.tsv.gz > fragments.tsv #...

To download everything (except all database feather files) with directory structure, you can use: ```bash wget --recursive --timestamping --no-parent -R '*.feather,*.zsync' https://resources.aertslab.org/cistarget/ ``` Downloading all Feather files by default is...

Probably the feather files you downloaded, where incomplete or corrupted.

With Numpy 1.23, the old syntax should still be supported: `pip install numpy=1.23`

@TheRaspberryFox Should be fixed in lastest git version: https://github.com/aertslab/scenicplus/commit/3741a4bbb1d8360d769d6aa22d02806e87a33b10