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pod5 filter freeze #95
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Hi @diego-rt , We're reworking We'll hopefully get this out before year end. However to help out in the meantime: It looks like you're running in
I hope these points help in the meantime and we'll get back to you soon with an update. Kind regards, |
Hi @HalfPhoton , Yes indeed I'm using nextflow with only one thread and 3G memory. I think the issue is that I've heavily parallelized it and have several hundred jobs simultaneously accessing the same file, which leads to some understandable I/O error. I should maybe reduce the number of forks, that's true. But I think the main problem is the fact that the process hangs without exiting. It would be fine if it just died with an error exit code because it just would retry, but since it does not actually exit, then the process just sits there until timeout. |
Yes you're absolutely correct and these changes will be incorporated to the new design of Best regards, |
Hello,
When running
pod5 filter
I often get a freeze for the process in a random manner. Rerunning it usually results in successful completion. It is annoying because it does not lead to an exit code or something so the process just hangs until timeout.This is the command:
This is the output:
Thanks!
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