diamond error! error code: -9

[fabrizziom99]

Hello, I was wondering if someone could help me. I´ve recently installed bakta via docker and when I use it, the process is killed and the following message pops up:

Traceback (most recent call last):
File "/opt/conda/bin/bakta", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/bakta/main.py", line 249, in main
cdss_psc, cdss_pscc, cdss_not_found = psc.search(cdss_not_found)
File "/opt/conda/lib/python3.8/site-packages/bakta/psc.py", line 64, in search
raise Exception(f'diamond error! error code: {proc.returncode}')
Exception: diamond error! error code: -9

[oschwengers]

Hi @fabrizziom99 ,
this might be a memory issue of Diamond. Could you try to execute the container with more memory? Normally 16 Gb is enough, but sometimes Diamond needs even more.

[fabrizziom99]

Indeed it was a memory issue, solved it by running bakta after upgrading my RAM. Thanks!!

[bio-Tao]

I see Diamond has option -b，

can add it for lower memory users?

[oschwengers]

Hi, sry, for the very late reply. Currently, this is not the case. We could maybe think about an automated adjustment based on free memory. But I'm a bit scared of potential side effects.

[Pashane240]

Hi, I'm having the same problem. I want to know how much RAM did you install to solve the issue?

[oschwengers]

Hi. Diamond's memory requirements within Bakta highly depend on the size/complexity of the genome and how many genes are actually searched, i.e. could not be identified via the AFSI approach.

Sometimes, even 8 GB is enough, but usually, we use 16 GB.
However, we regularly see a rare fraction of genomes for which we have to increase this limit to 32 GB.