Diamond Error -9

[cloeme]

Hi my error code is as below:

Traceback (most recent call last):
File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/bin/bakta", line 10, in
sys.exit(main())
File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/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 "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/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: -9

Ive tried running two separate genomes of bacteria and still the same error. I have plenty of memory and running this via Unix system (Spartan Unimelb)

Here were the steps to how I loaded Bakta:

Clone the bakta repository

git clone https://github.com/oschwengers/bakta.git

Go into the bakta directory

cd bakta

Copy FASTA file for your bacterial genome to conda environment

cp /data/cephfs/punim1258/chloe/new_rnaseq2024/4496_refgenome.fasta /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/

#load Anaconda or Miniconda module
module load Anaconda3/2024.02-1

#create a new conda environment
conda create -p /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv

#Run conda init in terminal
conda init

#source the updated file
source ~/.bashrc

#activate environment will show (base) at the front of script
conda activate /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv

the above steps creates the conda environment for running analysis /

#any packages installed while this environment is ACTIVE will be installed here specifically not affecting my base or other environments

Add the Bioconda channel

conda config --add channels conda-forge

Install Bakta packages

conda install bakta

Download the Bakta database

bakta_db download --output /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv --type full

Navigate to the directory containing your fasta file

cd /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv

Run the bakta tool on your fasta file

bakta --db /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/db 4496_refgenome.fasta --output /data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/bakta_output --force

Thanks in advance for the help

Chloe

[oschwengers]

Hi,
thanks for reporting. Have you already read and checked the issues/solutions provided here: #290 ?

[cloeme]

Hi, yes I have tried with the downgraded version but still receiving the same error:

found: 0

predict & annotate CDSs...
predicted: 2151
discarded spurious: 1
revised translational exceptions: 0
detected IPSs: 2038
Traceback (most recent call last):
File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/bin/bakta", line 10, in
sys.exit(main())
File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/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 "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/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: -9
(/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv) [cestoque@spartan-login2 myenv]$ diamond --version
diamond version 2.1.8

Thanks heaps for the help

[oschwengers]

OK, could you run Bakta setting the --debug flag and provide me the *.log file for a deeper look into this? And if possible, the genome file would also help to reproduce this error.