A ValueError when attempting to run Basenji

[jeffmylife]

When I attempt to run the Basenji model as in the example, this shows up:

`

pred = model.pipeline.predict_example()
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "", line 1, in
File "/anaconda3/lib/python3.6/site-packages/kipoi/pipeline.py", line 84, in predict_example
pred_list.append(self.model.predict_on_batch(batch['inputs']))
File "/anaconda3/lib/python3.6/site-packages/kipoi/model.py", line 1310, in predict_on_batch
feed_dict=merge_dicts(feed_dict, self.const_feed_dict))
File "/anaconda3/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 900, in run
run_metadata_ptr)
File "/anaconda3/lib/python3.6/site-packages/tensorflow/python/client/session.py", line 1111, in _run
str(subfeed_t.get_shape())))
ValueError: Cannot feed value of shape (10, 131072, 4) for Tensor 'inputs:0', which has shape '(2, 131072, 4)'
`

This occurred again when attempting to run the

(kipoi-Basenji) nsheng-mbp:Basenji jeffrey$ kipoi predict Basenji
--dataloader_args='{'intervals_file': 'example_files/intervals.bed', 'fasta_file': 'example_files/hg38_chr22.fa'}'
-o '/tmp/Basenji.example_pred.tsv'

Not sure how to fix this one. Any help is appreciated.

[Avsecz]

Hi, add a flag: --batch_size=2. The current implementation of basenji hardcodes the batch size.

[Avsecz]

I'll fix the code snippet on the website soon: kipoi/website#69

[jeffmylife]

I believe this worked for me.
Thank you for being so quick.