ValueError: Need a Nucleotide or Protein alphabet

[qianxin-kxy]

The following is the code I ran and the error situation. Has anyone encountered this issue? BioPython version is 1.77, and PhiSpy version is 4.2.21

(PhiSpy) [kxy@zju out]$ PhiSpy.py my_output.gbk -o output_directory
Processing 34 contigs
Making Testing Set...
Start Classification Algorithm...
Using the following metric(s): {'gc_skew', 'at_skew', 'shannon_slope', 'orf_length_med', 'max_direction'}.
Running the random forest classifier with 500 trees and 2 threads
/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py:870: FutureWarning: The default value of n_init will change from 10 to 'auto' in 1.4. Set the value of n_init explicitly to suppress the warning
warnings.warn(
As the training flag is zero, down-weighting unknown functions
Evaluating...
Checking prophages we might have found
Potential prophages (sorted highest to lowest)
Contig Start Stop Number of potential genes Status
NODE_25_length 4943 22015 29 Dropped. No genes were identified as phage genes
NODE_17_length 67767 91585 24 Kept
NODE_31_length 48 3971 8 Dropped. No genes were identified as phage genes
NODE_3_length 36724 41861 5 Dropped. No genes were identified as phage genes
NODE_7_length 40892 42026 2 Dropped. Region too small (Not enough genes)
NODE_9_length 147704 149860 1 Dropped. Region too small (Not enough genes)
NODE_9_length 128083 130272 1 Dropped. Region too small (Not enough genes)
NODE_8_length 31922 32392 1 Dropped. Region too small (Not enough genes)
NODE_2_length 90215 91141 1 Dropped. Region too small (Not enough genes)
NODE_27_length 8285 8959 1 Dropped. Region too small (Not enough genes)
NODE_20_length 9731 10882 1 Dropped. Region too small (Not enough genes)
NODE_18_length 55595 56515 1 Dropped. Region too small (Not enough genes)
NODE_17_length 38600 40714 1 Dropped. Region too small (Not enough genes)
NODE_16_length 41140 41724 1 Dropped. Region too small (Not enough genes)
NODE_15_length 34985 35749 1 Dropped. Region too small (Not enough genes)
NODE_11_length 62124 64214 1 Dropped. Region too small (Not enough genes)
PROPHAGE: 1 Contig: NODE_17_length Start: 67767 Stop: 91585
Creating output files
Writing GenBank output file
Traceback (most recent call last):
File "/data/users/kxy/miniconda3/envs/PhiSpy/bin/PhiSpy.py", line 10, in
sys.exit(run())
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 114, in main
PhiSpyModules.write_all_outputs(**vars(args_parser))
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/PhiSpyModules/writers.py", line 401, in write_all_outputs
write_genbank(self)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/PhiSpyModules/writers.py", line 98, in write_genbank
SeqIO.write(self.record, handle, 'genbank')
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/Bio/SeqIO/init.py", line 531, in write
count = writer_class(handle).write_file(sequences)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/Bio/SeqIO/Interfaces.py", line 235, in write_file
count = self.write_records(records, maxcount)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/Bio/SeqIO/Interfaces.py", line 209, in write_records
self.write_record(record)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/Bio/SeqIO/InsdcIO.py", line 1005, in write_record
self._write_the_first_line(record)
File "/data/users/kxy/miniconda3/envs/PhiSpy/lib/python3.10/site-packages/Bio/SeqIO/InsdcIO.py", line 757, in _write_the_first_line
raise ValueError("Need a Nucleotide or Protein alphabet")
ValueError: Need a Nucleotide or Protein alphabet

Additionally, because the ID in the gbk file obtained through the prokka annotation is too long, I used the following code to transform all LOCUS IDs in the file as follows:

LOCUS NODE_2_length_354722_cov_51.4144354722 bp DNA linear
sed -re 's/(_length)[^=]*$/\1/' 4751.gbk > my_output.gbk
LOCUS NODE_2_length

[linsalrob]

Can you share the original or modified GenBank file?