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deeptools / pyBigWig

A python extension for quick access to bigWig and bigBed files
MIT License
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Mismatch in the magic number when trying to open bigwig file to fix chromosome names #105

Closed WimSpee closed 4 years ago

WimSpee commented 4 years ago

Hi,

I am trying to use pyBigWig to fix chromosome names as described in this Biostar answer.

https://www.biostars.org/p/322341/

This results in the following error. 

python fix_big_chr_name.py  rename_chr.txt  input.bw output.bw
[readRTreeIdx] Mismatch in the magic number!
[bwOpen] bwg->idx is NULL bwg->hdr->dataOffset 0x259!
[pyBwOpen] bw is NULL!
Traceback (most recent call last):
  File "fix_big_chr_name.py", line 21, in <module>
    bw = pyBigWig.open(args.input)
RuntimeError: Received an error during file opening!

Is there a way to fix this, or at least to make if the input.bw file is correct?

Thank you.

dpryan79 commented 4 years ago

Are you sure args.input is actually a bigWig file? What does file input.bw return?

WimSpee commented 4 years ago

Hi Devon,

It turned out that the input file was corrupted by copying over a slow network connection. I recopied the file and then the renaming of the chromosomes via pyBigWig worked as expected. And I could finally load the file in our genome browser.

Thank you for the pyBigWig tool/library.