Metaspades terminated with an error exit status (21)

[ycuesta]

Description of the bug

Dear community.
We are running the mag pipeline and facing problems with the metaspades step.
The error looks like:
ERROR nextflow.processor.TaskProcessor - Error executing process > NFCORE_MAG:MAG:METASPADES
Caused by:
Process NFCORE_MAG:MAG:METASPADES terminated with an error exit status (21)

Thanks for the support!!! any idea about this issue with metaspades?
Yesid

Command used and terminal output

Relevant files

System information

No response

[ycuesta]

This is the print screen of the error:

In our case, MEGAHIT is running well, and we have the contigs from the assembly step. Are both programs (Spades and MegaHit) comparable in terms of accuracy? This is in case we cannot run spades and stay only with the MEGAHIT results.
Many thanks.
Yesid

[jfy133]

Hi @ycuesta 👋

You've only posted the top half of the error message so it's hard to say unfortunately.

It would be best if you could upload your .nextflow.log file which should have the whole error message.

Otherwise, both assemblers work pretty well.

Generally people say that megahit you get slightly higher quality contigs but are shorter, whereas metaspades gives you longer contigs but high risk of errors/misassemblies. So it depends what you need the contigs for, and what downstream steps to be performing - but this depends per researcher/project

[ycuesta]

Many thanks James.
Sorry. I will provide the .log files. On the other hand, we are pretending to retrieve MAGs from our shotgun data.
Many thanks.
Yesid