Spades finished abnormally, err code: -11

[piwczynski]

Hi,

I run getorganelle under various combination of parameters and always get the same error message from spades. Please, take a look. I provide you with getorganelle and spades log files.

Best
Marcin
spades.log
get_org.log.txt

[Kinggerm]

There are lots of "SPAdes finished abnormally, err -11" issues at SPAdes repo, where you may find the solution.

According to many replies, the SPAdes author was encouraging people compile SPAdes from source rather than from bioconda.

Let me know your updates.

[sivico26]

Just to add to the conversation, I solved the same problem updating Spades.

[nikolasjohnston]

Similar to @sivico26, I found that conda was not installing the most up-to-date version. Using conda update would not find the new version either

what worked for me was downloading version 3.15.3 from https://anaconda.org/bioconda/spades/files

Then installing using: conda install path/to/file

After this there was no issues running the software following the usual instructions.

[Kinggerm]

@nikolasjohnston @sivico26
Thanks for the feedback.

[V-Z]

I had same error when using SPAdes from GetOrganelleDep (cloning git repo as described on the wiki). When using custom SPAdes 3.15.2 it works well.

[Ruben9161]

Similar to @sivico26, I found that conda was not installing the most up-to-date version. Using conda update would not find the new version either

what worked for me was downloading version 3.15.3 from https://anaconda.org/bioconda/spades/files

Then installing using: conda install path/to/file

After this there was no issues running the software following the usual instructions.

Dear Nikolas,

I have a question: Did you install SPAdes apart from getorganelle?

Thanks for your feedback.

[nikolasjohnston]

Similar to @sivico26, I found that conda was not installing the most up-to-date version. Using conda update would not find the new version either
what worked for me was downloading version 3.15.3 from https://anaconda.org/bioconda/spades/files
Then installing using: conda install path/to/file
After this there was no issues running the software following the usual instructions.

Dear Nikolas,

I have a question: Did you install SPAdes apart from getorganelle?

Thanks for your feedback.

Hi @Ruben9161,

Yes I had to install SPAdes separately from getorganelle.

best,
Nik

[Kinggerm]

Sorry for the long delay.

As more users reported this issue, I feel obliged to update the GetOrganelleDep files to support the installation without conda. Here is the updated version: https://github.com/Kinggerm/GetOrganelleDep/releases/tag/v1.7.0

[JianjunJin]

@sue93653
#203

[Gymnosflora]

@JianjunJin, Thanks for your prompt reply. I will try to explore this. :-)