Spades assembly crashed without log error

[Fla1487]

Dear All,
I have a problem with unicylcer and short reads alignment by using spades.
I have previously used the same command without any troubles. Now with new sequences, and old ones, unicycler crashs.

Unicycler version: v0.5.0
Using 16 threads

Dependencies:
Program Version Status
spades.py 3.15.5 good
racon not used
makeblastdb 2.14.1+ good
tblastn 2.14.1+ good

This is the generated error (I have checked the log file without finding anything):

Error: SPAdes encountered an error:

Could You help to identify the problem?

Thank you in advance

[Fla1487]

I add also that follwoing uniclycler/spades guides, it is possible modify spades parameter, so that I added --spades options "-m 1024".
Unfortunatly I obtained:
unicycler: error: unrecognized arguments: --spades-options -m 1024

Honestly, I do not understand whats is the problem

Thank you again

[pwkooij]

@Fla1487 Not sure if it will resolve your problems, but I believe the correct argument should be --spades_options -m 1024

[marrip]

I have the same problem, did not try the option though...

[anaalmeidasantos]

Anyone manage to fix this? I got the same thing.

[pwkooij]

Anyone manage to fix this? I got the same thing.

Did you check whether the command was spelled correctly? (see my comment above)

[anaalmeidasantos]

Yes! I do this all the time and have only recently started encountering this error.

[pwkooij]

Can you show what the exact error is SPAdes is giving? It might be an issue with the swap space, which I had previously as well -> #300 (comment)

[anaalmeidasantos]

The error is the following:

WARNING: Try to use logger before create one. Level=ERROR. Message=File /hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info doesn't exist or can't be read!

== Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2

Something to do with the config.info file?

[pwkooij]

@anaalmeidasantos This looks similar to the error I had. Try increasing your SWAP, that might resolve it (it did for me)

[anaalmeidasantos]

I'm sorry, but I'm not very experienced with this. Could you guide me on how to increase my SWAP?

[pwkooij]

Are you running it locally or on a server?

[anaalmeidasantos]

On a server.

[pwkooij]

ok, then I have no idea, and not sure if that is the problem. Might be better to post the problem on the SPAdes github, since it's related to that.

I was running locally

[anaalmeidasantos]

Thank you for your help!

[niamhlacy]

Hi! I had the same problem and using using SPAdes 3.15.4 and python 3.9 solved it :)