Invalid interval bounds while generaing prediction bigwigs

[GalinaKoksharova]

Hello,

I'm trying to generate prediction bigwigs, but getting an error:"RuntimeError: Invalid interval bounds!".
My command looks like this:

chrombpnet pred_bw -cm chrombpnet_model.h5 -r bed10.bed -g hg38.fa -c hg38.chrom.sizes -op DNASE/GM12878 -bw ENCFF681PTG.bigWig

The model and the bigwig files were downloaded from https://www.encodeproject.org/annotations/ENCSR003WJE/ (the model was reformatted using reformat_chrombpnet_h5.py). I wanted to use bed3 file for the regions, so I tried to reformat it to bed10, according to the F.A.Q. (I'm attaching both here

bed10.txt
bed3.txt

)
Any insight on what could have gone wrong? I checked the chromosome sizes and end/start coordinates and they seem alright.

Thanks in advance,
Galina

[09oulin]

Hello,

I'm trying to generate prediction bigwigs, but getting an error:"RuntimeError: Invalid interval bounds!". My command looks like this:

chrombpnet pred_bw -cm chrombpnet_model.h5 -r bed10.bed -g hg38.fa -c hg38.chrom.sizes -op DNASE/GM12878 -bw ENCFF681PTG.bigWig

The model and the bigwig files were downloaded from https://www.encodeproject.org/annotations/ENCSR003WJE/ (the model was reformatted using reformat_chrombpnet_h5.py). I wanted to use bed3 file for the regions, so I tried to reformat it to bed10, according to the F.A.Q. (I'm attaching both here

bed10.txt bed3.txt

) Any insight on what could have gone wrong? I checked the chromosome sizes and end/start coordinates and they seem alright.

Thanks in advance, Galina

Have you solved it? I also met this problem. I will appreciate it if you can give me some precious advice.