Closed csoneson closed 3 years ago
Hi, thanks a lot for trying out cellstates - your feedback is much appreciated!
I fixed the problem with cell names in the simulated data - they are now cell_0001
, cell_0002
, etc.
tries_per_step
is a variable that is internally set, so it's just part of the normal running of the program - I understand though that it's a very confusing message so it will no longer be shown.
I also fixed the bug that caused your run to fail. However, I should note that the problems were probably caused because all simulated cells you selected for the test run come from the same cluster. You can find the true cluster labels in test_data/simulated_clusters.txt
(row 1 is cell_0000
, row 2 cell_0002
, etc).
Let me know if you still have any issues and thanks again for the feedback.
Thank you! I tried the new version on the example data and I can confirm that it now runs without errors. I will try it on my own data and get back to you if I run into any other issues.
Hi - I'm trying to run
cellstates
on the provided test data, and I'm running into some issues that I was hoping you could help me solve.The version of the software I used is the one from Feb 20. Installation went without problems.
Next, I was trying to run the software on the provided test data:
Here, I got some errors related to reading the file, which I think are due to the presence of spaces in the header (e.g.,
cell_ 1
rather thancell_1
):I removed the first 1,000 cells (the ones containing white spaces), and further subset to the first remaining 200 cells to speed things up (I don't think this is the reason for the problem, I got the same issues when running on the full set of cells except the first 1,000). Now, calling
run_cellstates.py
fails with the following error message:I could not find a way to change the
tries_per_step
variable. Could you provide some insights into what's going on here, and what would be the expected output of runningrun_cellstates.py
on the provided test data?Thanks!