Issue with the signal rejoining script and model 2 with the 4 dimensional issues about cheui HOT 3 OPEN

Hi,

I want to make an update on the signalling script. I sorted the signalling arguments but they took very long to proceed so I have skipped this script because I have limited runtime. I just ran the signal chunks straight to model 1 and combine the result afterwards. I wonder does it impact the downstream performance?

Second, I have an issue with the model 2 dimension issue in m5C predictions. My input file is 122G and I broke it down into the first 50000 lines for processing and it is still not working. I have checked the format and there are 3 columns: The transcript and the cytosine sites, a series of probability and the replicate tag. I double-checked there are no extra columns or data that is not aligned properly. The model ran smoothly for the first few minutes, but it stopped in the middle and reported the dimension issue:

"W tensorflow/core/framework/op_kernel.cc:1828] OP_REQUIRES failed at conv_ops_fused_impl.h:761 : INVALID_ARGUMENT: convolution input must be 4-dimensional: [1,32,99]"

I have tried adding a fourth column with '1's to fulfill the requirement, and removing the replicate tag column as the test data only has 2 columns, but the wrong format error will come up. Can you try to resolve it, please?

Dom

from cheui.

Hi,

Sorry about the run time issue. We are working on the faster preprocessing version and will have the update soon.
I think its ok to pass chunks to model1 and combine output at the end as you mentioned. Sort them before passing to model2.

i think the issue you are getting regarding the dimension is because of TensorFlow version. What version are you using ?

Either please install the recommended version TF 2.4.1

Or

please try replacing the below line in the CHEUI_predict_model2.py code

lr_probs = model.predict(prob_vectors)
to:
lr_probs = model.predict(prob_vectors.reshape(prob_vectors.shape[0], 99, 1))

It should be line number 199 and 220 in CHEUI_predict_model2.py.

Please let us know if it helps.

Thanks,
Akanksha

from cheui.

Hi Akanksha,

Thank you so much for your reply.

That is absolutely fine and totally understandable that it takes time to develop the new preprocessing script and I will finger-cross it for the CHEUI team.

That is great! I just want to make sure the result is not disrupted even if I am not following the combined script. Regarding model 2, I added the reshaped part for the Ir_probs. I think it is working properly and does generate much longer results now.

Bw,
Dominic

from cheui.