none results generating with huge dump files

[zhengyanstu]

Dear developers,
I encountered some issues while using Smudgeplot to predict polyploidy. The species I am studying is expected to be hexaploid based on flow cytometry analysis, but whether it is autopolyploid or allopolyploid is unknown. The size of the dump file extracted using Jellyfish is 16GB, and smudgeplot.py hetkmers stage has been running for several days without producing any results, although the program is indeed running. I extracted 2GB of data from the dump file and ran it again, but the prediction still shows a diploid AB type. Can you please help identify the cause of this issue and suggest any methods to speed up the process?
The remaining free RAM more than 500G.

[xujialupaoli]

Hi Kamil,

Thanks for the clear documentation and awesome tool.
I also encountered a similar problem.I would like to know if the species I am studying is diploid or tetraploid. I got about 40G *.jf file through jellyfish histo. But now smudgeplot.py has been running for a long time, but no result file has been obtained. I really hope there is a way to speed up the progress.

[KamilSJaron]

Hi hi, sorry for the silence, I am on a paternity leave.

We are very close to release a new version, which is now stalled for rising an offspring, but it's actually a well functioning version. If you take a look at the BGA23 tutorial, we already thought the update. THe new updated version is about 100000x faster (I exaggerate a bit, but just a bit - it's really a lot faster, the backend is written by Gene Myers). Anyway, if you take a loot at that, you might be able to run smudgeplot on a lot bigger genomes in a fraction of time: https://bga23.org/smudgeplot/

[tallnuttrbgv]

How does the bga link address this problem? I cannot find a solution there. Thanks.

[tallnuttrbgv]

Is this software no longer supported?

[KamilSJaron]

Is this software no longer supported?

Ehm? Are you serious?

[KamilSJaron]

How does the bga link address this problem? I cannot find a solution there. Thanks.

It explains how to work with a development version of the software. If it's not clear enough for you, you have to wait for a proper release I am afraid.