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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Exception: diamond error! error code: -11 #271

Closed jjpadilla1987 closed 9 months ago

jjpadilla1987 commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

Hi @simone-pignotti and @oschwengers,

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

pcrxn commented 9 months ago

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 commented 8 months ago

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.

https://github.com/bbuchfink/diamond/issues/785

oschwengers commented 8 months ago

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