Jianjun Jin

Sorry for the delay. I just posted an update on FAQ https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#memoryerror I would first try using `--memory-save` and `-w 195`. BTW, your dataset looks difficult, with a huge dataset...

The absolute coverage of 262.96 is definitely enough for any organelle genomes, but it was estimated based on 37.5G of the 108G data, meaning that the ratio is very low....

I'm working on developing GetOrganelle for long reads. Leave this issue open and I will let you know the updates. Currently, you can use Flye to assemble a certain amount...

> jaktykusuma Your error was different from the current thread. The deprecated dependency issue is currently a harmless warning, not an error. The failure of running SPAdes in your case...

> Hi, > > I have installed using a manual method - git clone etc. But it seems to fail on test data building the bowtie index. > > Thanks,...

I would try removing SPAdes under GetOrganelleDep rm -r /g/data/nm31/bin/GetOrganelle/GetOrganelleDep/linux/SPAdes/ Then install the latest SPAdes using `apt install`, or `conda`, or from the source. Let me know your updates.

BTW, no matter if the latest SPAdes could fix your issue on the Gadi environment or not, the GetOrganelleDep needs an update. I will leave this issue open until an...

What is the result of `spades.py --test`?

`to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf'`

You should reduce the input reads. Check the illustration of `--reduce-reads-for-coverage` and `--max-reads`.