diamond error! error code: 1 with pseudogenes

[michoug]

Hi,
I tried to annotate the publically available genome https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001313365.1/

Which apparently had a lot of issues so the error I got may be due to this

I ran bakta tens of times on other genomes using the same version and never had an issue.

Here is the debug log

Bakta v1.10.4
Options and arguments:
	input: /home/river/Desktop/Greg/test/AnalysesResult/Pseudoarthrobacter_45_clean/neighbors/GenomesClose/GCA_001313365.1_ASM131336v1_genomic.fna
	db: /home/river/Desktop/Databases/Bakta/db, version 5.1, full
	translation table: 11
	output: /home/river/Desktop/Greg/test/AnalysesResult/Pseudoarthrobacter_45_clean/neighbors/GenomesClose/GCA_001313365.1_ASM131336v1_genomic/Annotations
	force: True
	tmp directory: /tmp/tmpy5nkfpyd
	keep/sequence headers: True
	prefix: GCA_001313365.1_ASM131336v1_genomic
	threads: 8
	debug: True

Bakta runs in DEBUG mode! Temporary data will not be destroyed at: /tmp/tmpy5nkfpyd

Parse genome sequences...
	imported: 238
	filtered & revised: 197
	contigs: 197

Start annotation...
predict tRNAs...
	found: 54
predict tmRNAs...
	found: 1
predict rRNAs...
	found: 3
predict ncRNAs...
	found: 3
predict ncRNA regions...
	found: 22
predict CRISPR arrays...
	found: 0
predict & annotate CDSs...
	predicted: 9099 
	discarded spurious: 15
	revised translational exceptions: 0
	detected IPSs: 121
	found PSCs: 717
	found PSCCs: 1994
	lookup annotations...
	conduct expert systems...
		amrfinder: 1
		protein sequences: 0
	combine annotations and mark hypotheticals...
	detect pseudogenes...
		candidates: 1334
Traceback (most recent call last):
  File "/home/river/Desktop/Greg/test/snakemake_envs/bb6f6e18a5017a2d2a02d4a1b339be34_/bin/bakta", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/river/Desktop/Greg/test/snakemake_envs/bb6f6e18a5017a2d2a02d4a1b339be34_/lib/python3.11/site-packages/bakta/main.py", line 325, in main
    pseudogenes = feat_cds.detect_pseudogenes(pseudo_candidates, cdss, data) if len(pseudo_candidates) > 0 else []
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/river/Desktop/Greg/test/snakemake_envs/bb6f6e18a5017a2d2a02d4a1b339be34_/lib/python3.11/site-packages/bakta/features/cds.py", line 681, in detect_pseudogenes
    raise Exception(f'diamond error! error code: {proc.returncode}\n{proc.stdout}')
Exception: diamond error! error code: 1

You can find the temporary folder here

https://1drv.ms/u/s!AsMX6oHOc4zYusNeUifh7v9nDOdUog?e=Sp7TmS

Best
Greg