Generating contribution score bigwig file
PetHabib opened this issue · 5 comments
Hi,
when I tried to generate the contribution score, chromebpnet was able to generate all files (*.counts_scores.h5, *.interpret.args.json, *.interpreted_regions.bed, *.profile_scores.h5) except .bw one and it did not generate any error, do you have any idea why this happened?
Thank you in advance.
Hi Peter,
I think we need to update our chrombpnet installation to version 0.1.5 - which is the latest version. I also got the same error and then I noticed in the change log - v0.1.4...v0.1.5
@panushri25 - is updating to the newest version the correct solution for the error below?
Error using v0.1.4 while running the contribution score step-
2023-12-08 01:15:08.482486: I tensorflow/stream_executor/cuda/cuda_blas.cc:1786] TensorFloat-32 will be used for the matrix multiplication. This will only be logged once. Traceback (most recent call last): File "/users/sen2qb/conda_env/chrombpnet_oct_2023/bin/chrombpnet", line 8, in <module> sys.exit(main()) File "/users/sen2qb/conda_env/chrombpnet_oct_2023/lib/python3.8/site-packages/chrombpnet/CHROMBPNET.py", line 68, in main importance_hdf5_to_bigwig.main(args_copy) File "/users/sen2qb/conda_env/chrombpnet_oct_2023/lib/python3.8/site-packages/chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py", line 30, in main regions = bigwig_helper.get_regions(args.regions, SEQLEN) TypeError: get_regions() missing 1 required positional argument: 'regions_used'
Hey Sid,
Thank you very much for letting me know! I will update and see if it solves this.
Thanks @PetHabib for your answer.
Yes thats correct, please upgrade to the latest version for fixing this.
I am going to release another version in a bit, will keep you posted here. So you can upgrade to that.
Please update to the latest 0.1.6 version and regenerate your contribution scores. It should fix this error, 0.1.5 has an incorrect and incomplete fix.
Great - thanks for the quick resolution!