TypeError: get_regions() missing 1 required positional argument: 'regions_used'
MZZheng opened this issue · 8 comments
Hello
I used "chrombpnet bias pipeline" train my model, and then use
" chrombpnet contribs_bw -m ./results/models/bias.h5 -r hudep2_1.narrowPeak -g hg19.fa -c hg19.chrom.sizes -op hudep2_scores_"
to get the contribution scores. But I get an error:
Saving 'profile' scores
Traceback (most recent call last):
File "/home/mzheng09/.conda/envs/chrombpnet/bin/chrombpnet", line 8, in
sys.exit(main())
File "/home/mzheng09/.conda/envs/chrombpnet/lib/python3.8/site-packages/chrombpnet/CHROMBPNET.py", line 68, in main
importance_hdf5_to_bigwig.main(args_copy)
File "/home/mzheng09/.conda/envs/chrombpnet/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'
Can you help me figure out how to fix the error? Thank you very much.
Hello, which version of chrombpnet are you running
I installed the chrombpnet a week ago, using the method as below:
##Create a clean conda environment with python >=3.8
conda create -n chrombpnet python=3.8
conda activate chrombpnet
##Install non-Python requirements via conda
conda install -y -c conda-forge -c bioconda samtools bedtools ucsc-bedgraphtobigwig pybigwig meme
oh okay, can you update it? I made a new release that should fix this
just do pip install chrombpnet --upgrade in the environment i.e do conda activate chrombpnet first.
OK, thank you so much!
Also I recommend you add yourselves to the watchers list on the github page. You will get notified of any changes made to the repo.
Please update to the latest 0.1.6 version and regenerate your contribution scores. It should fix this error.
Let me know if you see any more issues.