RuntimeError: Invalid interval bounds! about pybigwig

[dpryan79]

> import pyBigWig
> bw = pyBigWig.open("https://www.encodeproject.org/files/ENCFF743ULW/@@download/ENCFF743ULW.bigWig")
> bw.chroms("chr2")
242193529L

So that's why you get the error and how you can check chromosome sizes.

[zoink]

Thanks, the DNase-seq file I was using was mapped against hg38 (chr2 length=242193529) , but the intervals were derived from hg19 (chr2 length=243199373).

[shamsbhuiyan]

Hello, I am hit with a similar issue. However, I am using the same build and I've double checked the length of chromosome 6.

Traceback (most recent call last):
  File "find_sORFs.py", line 245, in <module>
    compute_phylop_score("five_prime_sORFs.bed",human_phylop_bigwig)
  File "find_sORFs.py", line 222, in compute_phylop_score
    vals = bw.values(cols[0], int(cols[1]), int(cols[2]))
RuntimeError: Invalid interval bounds!

This breaks at 'chr6', '83707928', '83707957', but the length of chromosome 6 according bw.chroms("chr6") is 170805979. Any thoughts?

[Jome0169]

Hi @shamsbhuiyan did you ever figure this out? Getting the same error and can't figure out what might be causing it.