ValueError: cannot reshape array of size 0 into shape (0,newaxis)

[yeeus]

In the last step to predict gene expression, I got an error:

Traceback (most recent call last):
  File "path/SVEN/predict_expression.py", line 89, in <module>
    model_prediction("ref")
  File "path/SVEN/predict_expression.py", line 36, in model_prediction
    anno_whole = anno_whole[:, :, filter_index].reshape(anno_whole.shape[0], -1)
ValueError: cannot reshape array of size 0 into shape (0,newaxis)

I'm not sure what happened due to such a huge project...

[XL-1748]

I'm having the same problem.

[freshmanfresh]

@yeeus Could you provide more specific information on this: your input and what commands you execute?

[yeeus]

You can try this test file test.vcf.gz.
All I did was follow your instruction about predicting effects of SVs on gene expression level.
And in the last step I got above error.

Acturally, I got another error in the step prepare_data.py, but it seemed everything was normal and I got the outputs for the next step.

python ~/softwares/SVEN/prepare_data.py --type sv test.vcf
path/mambaforge/envs/sven/bin/bedtools
##### Success: extract bed file. #####
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoll
##### Success: extract sequences from bed file. #####
##### Processing 0 sequence pairs. #####
##### Success: sequence one-hot encoding. #####

[yeeus]

Actually this SV was within a gene... :-(

[XL-1748]

But, I was using your test_sv.vcf file and followed your process (predicting SV effect on gene expression levels) and got the same error.

[freshmanfresh]

@yeeus @XL-1748 I have identified the error. The error was with bedtools. You can install bedtools 2.26.0 by conda install bioconda::bedtools=2.26.0 . We have also updated Installation document and prepare_data.py. Can you update files and bedtools and try again?

[XL-1748]

After updating, no errors were reported in the previous steps, but the same error as before occurred in the last step (using the test_sv.vcf )
`##### Predict with fast mode... #####

Loading annotations...

Traceback (most recent call last):
File "/home/ubuntu/liuhong/SVEN-0.1.0/SVEN-0.1.0/predict_expression.py", line 89, in
model_prediction("ref")
File "/home/ubuntu/liuhong/SVEN-0.1.0/SVEN-0.1.0/predict_expression.py", line 36, in model_prediction
anno_whole = anno_whole[:, :, filter_index].reshape(anno_whole.shape[0], -1)
ValueError: cannot reshape array of size 0 into shape (0,newaxis)`

[freshmanfresh]

@XL-1748 Can you provide all commands and full outpus (including previous steps) as a log file?

[XL-1748]

test_sv1.log

[freshmanfresh]

@XL-1748 you should remove the work dir work_dir and then run the codes. I will add "remove temp files" function later.