New version of bakta v1.10 fails to run annotations

[Dx-wmc]

Hi, I upgraded to version 1.10 using conda (the version 1.9 environment cannot be upgraded directly). When I tried to run the genome that could be run successfully in the previous version, it got an error.

The command I used: bakta K130.fasta --prefix K130 --output K130_bakta --min-contig-length 200 --locus-tag K130 -t 16 --keep-contig-headers --force

/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
Bakta v1.10.0
Options and arguments:
	input: /home/data/usr/dx/workdir/test/bakta/K130.fasta
	db: /home/data/public/database/bakta/db, version 5.0, full
	translation table: 11
	locus tag prefix: K130
	output: /home/data/usr/dx/workdir/test/bakta/K130_bakta
	force: True
	tmp directory: /tmp/tmp4ifivcfw
	keep/sequence headers: True
	prefix: K130
	threads: 16
	debug: True

Bakta runs in DEBUG mode! Temporary data will not be destroyed at: /tmp/tmp4ifivcfw

Parse genome sequences...
	imported: 210
	filtered & revised: 210
	contigs: 210

Start annotation...
predict tRNAs...
	found: 83
predict tmRNAs...
	found: 1
predict rRNAs...
	found: 13
predict ncRNAs...
	found: 93
predict ncRNA regions...
	found: 57
predict CRISPR arrays...
	found: 0
predict & annotate CDSs...
	predicted: 5682 
	discarded spurious: 6
	revised translational exceptions: 3
	detected IPSs: 5515
	found PSCs: 128
	found PSCCs: 16
	lookup annotations...
	conduct expert systems...
		amrfinder: 31
		protein sequences: 244
	combine annotations and mark hypotheticals...
	detect pseudogenes...
		candidates: 9
		verified: 1
	analyze hypothetical proteins: 39
		detected Pfam hits: 1 
		calculated proteins statistics
	revise special cases...
detect & annotate sORF...
	detected: 57570
	discarded due to overlaps: 44771
	discarded spurious: 0
	detected IPSs: 34
	found PSCs: 1
	lookup annotations...
	filter and combine annotations...
	filtered sORFs: 28
detect gaps...
	found: 0
detect oriCs/oriVs...
	found: 6
detect oriTs...
	found: 2
apply feature overlap filters...
select features and create locus tags...
	selected: 5954
improve annotations...
	revised gene symbols: 33

Genome statistics:
	Genome size: 5,923,825 bp
	Contigs/replicons: 210
	GC: 56.8 %
	N50: 121,978
	N ratio: 0.0 %
	coding density: 87.7 %

annotation summary:
	tRNAs: 82
	tmRNAs: 1
	rRNAs: 13
	ncRNAs: 93
	ncRNA regions: 57
	CRISPR arrays: 0
	CDSs: 5674
		hypotheticals: 38
		pseudogenes: 1
	sORFs: 26
	gaps: 0
	oriCs/oriVs: 6
	oriTs: 2

Export annotation results to: /home/data/usr/dx/workdir/test/bakta/K130_bakta
	human readable TSV...
	GFF3...
	INSDC GenBank & EMBL...
Traceback (most recent call last):
  File "/home/data/usr/dx/miniconda3/envs/bakta/bin/bakta", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/bakta/main.py", line 543, in main
    insdc.write_features(data, features, genbank_path, embl_path)
  File "/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/bakta/io/insdc.py", line 292, in write_features
    sequence_list = build_biopython_sequence_list(data, features)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/bakta/io/insdc.py", line 248, in build_biopython_sequence_list
    qualifiers['note'].append("(3' truncated)")
    ^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'append'

In addition, when running only bakta -h, there will still be warning messages.

/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/home/data/usr/dx/miniconda3/envs/bakta/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  return self._float_to_str(self.smallest_subnormal)

The fasta file and the log file I have attached below.
fasta+log.zip

[mjfos2r]

I am also getting the NumPy warning. It appears to be related to some dependency somewhere that's compiled with -ffast-math but I've no clue which it could be.

Annotation is working for me despite this.

[oschwengers]

Hi @Dx-wmc and @mjfos2r,
thanks for reporting. There are two distinct issues occurring here:

1. There is a true bug that caused the above reported crash. This is fixed by 5e7f09f and 6332cfd
2. Though no real bugs, there are some very annoying warnings which are caused by ffast-match compilation flag as pointed out by @mjfos2r . Unfortunately, I also have no clue what exactly is causing this. I can only hope that someone has a clue or over time, this will be fixed upstream.

Together with the fix for #342, I'll release a patch very soon. To separate reports, I've filed a dedicated issue for the warning messages and close this. For everything related to the warnings, please feel free to jump over to #347.