Error assembling the Arabidopsis test dataset (SPAdes errors)

[jsmillergh]

Hello,

I am attempting to assemble the Arabidopsis plastome using the provided test dataset (simulated Arabidopsis thaliana WGS dataset). After (i) installing/updating GetOrganelle, (ii) initializing the organelle type, and (iii) running GetOrganelle, I believe I see two SPAdes errors in the log file but am not sure how to resolve them.

Both the GetOrganelle and the SPAdes log files are attached.

A great many thanks for advice or assistance.

-Jill

get_org.log.txt
spades.log

[Kinggerm]

What is the outcome of spades.py --test?

[jsmillergh]

Thanks! I ran spades.py --test and attached is the terminal output & the spades log. -Jill
Terminal Saved Output.txt
spades.log

[Kinggerm]

It looks like a SPAdes issue. Please reinstall SPAdes to make sure it passes the test.

[JianjunJin]

Have you fixed the SPAdes problem?

[jsmillergh]

Thanks for your message (& your program!), but sadly I have not been able to resolve. The SPAdes folks told me to install the latest version to see if the error persisted, but that version (3.15.5) was not installable following their instructions <https://github.com/ablab/spades/blob/spades_3.15.5/README.md#sec2.2>. In the meantime, I am using getorganelle on my previous laptop and will have to run the program from that machine. Thanks, Jill S. Miller Professor of Biology & Thomas F. Pick Reader in Environmental Studies Amherst College | Amherst, MA 01002 | USA Tel. 413-542-2168 | ***@***.***

…

On Jan 24, 2023, at 12:23 AM, JianjunJin ***@***.***> wrote: Have you fixed the SPAdes problem? — Reply to this email directly, view it on GitHub <#226 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5DW3WN6TQJUL6MUEJNFONDWT5RLPANCNFSM6AAAAAATTNVSGA>. You are receiving this because you authored the thread.

[Kinggerm]

Sorry to hear that it still bothers you.
If I were you, I might try the older versions of SPAdes.