Open Chrisdoan9 opened 8 months ago
Are you sure the filenames you made, exist? What is the output of:
# 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
assert os.path.isfile(fname), """Database "{fname}" doesn't exist."""
To:
assert os.path.isfile(fname), f"""Database "{fname}" doesn't exist."""
So you can see about which filename it complains.
Or install the lastest git version of ctxcore:
pip install 'ctxcore @ git+https://github.com/aertslab/ctxcore'
Hi @ghuls, the file name I download were a little different with the file name in the tutorial which caused the error. Thank you so much! However, I ran into another issue. After a long running time with the cell above, I got kernel death with this in the log file:
Saving file at /project/multiome.ipynb
[I 15:44:24.645 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
Would you please have a suggestion? I had all the output in the tutorial. Is there anyway I can save everything so if I got error like this, I don't have to run again from the beginning? May I know how much memory I need to run this tutorial?
Hi all,
I downloaded 3 files required but still got fname doesn't exist error. Would you please have a look? Thank you so much!
Describe the bug AssertionError: Database "{fname}" doesn't exist.
To Reproduce
Expected behavior 2022-08-05 08:53:16,277 pycisTarget_wrapper INFO pbmc_tutorial/motifs folder already exists. 2022-08-05 08:53:17,650 pycisTarget_wrapper INFO Loading cisTarget database for topics_otsu 2022-08-05 08:53:17,653 cisTarget INFO Reading cisTarget database 2022-08-05 09:13:51,198 pycisTarget_wrapper INFO Running cisTarget for topics_otsu
Version (please complete the following information):