Exception: diamond error! error code: -11

[jjpadilla1987]

I am trying to annotate multiple genomes and used bakta since I already used this tool before and it worked well and gave out the best results compared to other tools. However, I have been encountering problems lately when running the analysis, I already tried to re-install bakta but it didnt work. Here's the code i used:

bakta --db /work/jpadilla/conda/envs/bakta/db --prefix 2008Ycf657 --output bakta_2008Ycf657 --genus Burkholderia --species cenocepacia --strain 2008Ycf657 --complete --keep-contig-headers --compliant --force --translation-table 11 --threads 20 2008Ycf657.fna

And here's is the error I got:

parse genome sequences...
imported: 3
filtered & revised: 3
chromosomes: 3

start annotation...
predict tRNAs...
found: 70
predict tmRNAs...
found: 1
predict rRNAs...
found: 18
predict ncRNAs...
found: 33
predict ncRNA regions...
found: 23
predict CRISPR arrays...
found: 0
predict & annotate CDSs...
predicted: 6815
discarded spurious: 1
revised translational exceptions: 1
detected IPSs: 6517
Traceback (most recent call last):
File "/work/jpadilla/conda/envs/bakta/bin/bakta", line 10, in
sys.exit(main())
File "/work/jpadilla/conda/envs/bakta/lib/python3.10/site-packages/bakta/main.py", line 259, in main
cdss_psc, cdss_pscc, cdss_not_found = psc.search(cdss_not_found)
File "/work/jpadilla/conda/envs/bakta/lib/python3.10/site-packages/bakta/psc.py", line 64, in search
raise Exception(f'diamond error! error code: {proc.returncode}')
Exception: diamond error! error code: -11

[simone-pignotti]

Hi, I am running into the same issue. Downgrading Diamond from 2.1.9 (released last week) to 2.1.8 has solved the problem for me, but looking at the changelog for 2.1.9 I don't see any breaking changes which might be at the root of this...

[oschwengers]

Thanks @simone-pignotti for the heads-up.
@jjpadilla1987 could you check, if downgrading Diamond to v2.1.8 solves the error in case, as well?

[jjpadilla1987]

Hi @simone-pignotti and @oschwengers,

Thanks for the suggestions. I installed diamond 2.1.8 and the analysis worked!

[pcrxn]

I'm experiencing the same error when attempting to analyze GCA_003339035.1, and I can also confirm that downgrading Diamond to v2.1.8 fixes the error. See bakta_diamond-2.1.9.stdout.txt and bakta_diamond-2.1.8.stdout.txt attached.

[oschwengers]

FYI, this bug is occurring in Diamond and it has been reported upstream. A downgrade to v2.1.8 is currently the best we can do until this is fixed.

bbuchfink/diamond#785

[oschwengers]

FYI: I temporarily pinned Diamond to v2.1.8 in the Bakta Bioconda package: bioconda/bioconda-recipes#46111