Martin Steinegger

Thanks a lot! How much memory does your machine have? Normally Plass try to split the database if it does not fit in memory.

So it seems that the extractorfs step is hanging, which mostly requires IO. Is it possible that the tmp folder is on some slow network share? One trick to reduce...

Do you use a grid engine and the job might have timed out? Your log outputs "killed" after the 6th iteration. So the OS or the grid engine might have...

@apcamargo I really do not know whats the issues. Some times it runs only one iteration and then six. Is it possible to share the data? I would try to...

@apcamargo thank you trying Plass. Yes it is hard to reliably call short genes and distinguish the frames correctly. We set the threshold of our NN to not harm the...

@apcamargo Thank you again for your insightful analysis. We added a remark in the README of Plass. See: https://github.com/soedinglab/plass/blob/master/README.md

@apcamargo great to hear! Currently I do not work on it. But I am happy to help integrating the networks if needed.

@liuxianghui Plass extract all open reading frames from short reads and extending them through overlap detection. This works well for proteins that are encoded in an consecutive way. However, eukaryotes...

Yes I would love to have this as well. 👍 But so far I did not come up with an solution how I could gather this information. It is hard...

@apcamargo yes this a good idea. But do you know if EM would be fast enough to handle this large amount of data?