nanoporetech/pod5-file-format

broken pipe error when running pod5

Flower9618 opened this issue · 5 comments

Flower9618 commented

Hi, when I try to run pod5 v0.1.13 to convert .fast5 to .pod5, there is an error:
image

Anyone has some advice? Thank you very much!

Flower9618 commented

I run dorado ... && touch one log file. Interestingly, although there is an error about broken pipe, the log file is created. I would like to know whether dorado succeed or failed?

HalfPhoton commented

Hi @Flower9618, from the command it looks like you're running pod5 convert fast5 and it appears to have raised this error right at the very end. As the conversion step looks like it's finished, could you check that all of the pod5 files which were generated here are complete, running pod5 inspect summary over the outputs.

To help us with tracking down this error, could you share with us;

  • The full command was run
  • Your operating system
  • The pod5 --version

We'll look into this issue now.

Thanks

HalfPhoton commented

Thanks for reporting this issue.
We've isolated this bug and are issuing a fix in 0.1.14 imminently.

HalfPhoton commented

This issue should now be resolved in the latest 0.1.15 release.

Thanks again for reporting this issue.

Best regards,
Rich

maxim-h commented

For people that may still stumble on a similar problem. I've been running pod5 convert fast5 with --one-to-one option and got the BrokenPipeError as well.
Turns out that the output directory contained some files from a previous interrupted run. Clearing the output directory from any files solved the issue.