Error processing message when running pod5 convert fast5 about pod5-file-format HOT 10 CLOSED

Hi, @HalfPhoton
I try pod5 convert fast5 command on the same sample as before, and it runs successfully. Thank you very much !

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@HalfPhoton , thank you so much. I will try it. :)

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it may be related to #33

Or maybe can you check how large your dataset is and whether there is enough diskspace available (in the working directory)?

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Hi, @sklages . Thank you for your reply.
It seems not the memory or disk problem.
This is the detail about the error. When converting 30%, the speed is fast. But when converting 80%, the speed is quite slow, and when I top, there is no pod5 command running.

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@Flower9618 - the same here. And you're right, it's not a disk space issue. After all I came to the same conclusion. #33

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Hi, @sklages .
Thank you very much. I see. So it seems even if I set the --threads 1, it will not work. The only way to do it is breaking fast5 files into chunks...but this is inconvenient for large amounts of data...:(

from pod5-file-format.

Thanks for bringing this to our attention.

There are a number of changes to convert fast5 which are review which should hopefully improve performance. Including removing the initial multi-read fast5 check stage.

Thank you for your patience with us while we resolve these issues.

We'll let you know as soon as we get a tagged release out.

Kind regards,
Rich

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@HalfPhoton .
Thank you so much. I am looking forward to it.

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@Flower9618, I'm pleased to say we released 0.1.19 last night, which should contain fixes for your issue. Could you please give it a go and let us know if this patch has resolved your issues?

Kind regards,
Rich

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@Flower9618 , I'm very happy to hear that! Thanks for letting us know that it's fixed 😃

Thanks again,
Rich

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