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smithlabcode / dnmtools

Tools for analyzing DNA methylation data
https://dnmtools.readthedocs.io
GNU General Public License v3.0
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bad count line #191

Closed masarunakajima closed 12 months ago

masarunakajima commented 12 months ago

Describe the bug Running hmr for SRX9736058 results in error:

[E::bgzf_read_block] Failed to read BGZF block data at offset 47705490 expected 9769 bytes; hread returned 4700
bad count line: chr8  10716735
[Tue Nov 28 22:08:20 2023]

To Reproduce Steps to reproduce the behavior:

  1. For the above experiment, run
  2. dnmtools abismal to map
  3. dnmtools format
  4. samtools sort
  5. samtools merge
  6. dnmtools uniq
  7. dnmtools count
  8. dntmools sym
  9. dnmtools hmr

Expected behavior Outputs hmr

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

masarunakajima commented 12 months ago

This could simply be due to a process interrupted resulting in incomplete input file.