Error during spades assembly about getorganelle HOT 5 CLOSED

Hi Todd,

Can you post the complete log files of GetOrganelle and SPAdes here or send them to my email?

Cheers,
Jianjun

from getorganelle.

Hi Jianjun,

Thanks for your response. I've attached the log files for both GetOrganelle and Spades.

Cheers,
Todd

GetOrganelle.15134537.txt
spades.log

from getorganelle.

Hi Todd,

I took a look at your log files. I'm sorry I cannot figure out why SPAdes crashes. I googled for SPAdes with "err code: -8" but find nothing related.
Could you try your data with another server? I can see that your data is small enough to be run on most linux/Mac laptop with GetOrganelle, which should not take more than 30 minutes.

By the way, -w 103 could be too large for a small dataset, but, since you still have plenty of reads captured at this moment, you don't really need to change it. But if you find your plastome contigs to be unconnected in the graph, try -w 95 or a smaller value.

Best,
Jianjun

from getorganelle.

Hi Jianjun,

I wonder if 'error code: -8' is a default linux error code? I will try it on another computer and see if it completes. I have run several other softwares which include spades and have not run into any errors.

Thanks for your suggestions,,
Todd

from getorganelle.

Hi Todd,

Have you went through it?

Best,
Jianjun

from getorganelle.