IndexError: list index out of range error

[hbucqp]

Hi, I am trying to use Platon 1.6 installed with BioConda to identify plasmid contigs. By running the following command:

platon --db ~/database/db --prefix test --output ./ test.fa

Platon reports a IndexError: list index out of range

Traceback (most recent call last):
  File "/home/cui/miniconda3/envs/platon/bin/platon", line 10, in <module>
    sys.exit(main())
  File "/home/cui/miniconda3/envs/platon/lib/python3.8/site-packages/platon/platon.py", line 153, in main
    proteins_path = pf.predict_orfs(contigs, cfg.genome_path)
  File "/home/cui/miniconda3/envs/platon/lib/python3.8/site-packages/platon/functions.py", line 492, in predict_orfs
    orf_id = cols[8].split(';')[0].split('=')[1].split('_')[1]
IndexError: list index out of range

The version of dependent software is

• Prodigal: V2.6.3
• diamond: V2.0.15
• blastn: V2.13.0+
• hmmsearch: V3.3.2
• nucmer: V4.0.0
• cmscan: V1.1.4

The fasta file I used is test.zip

[oschwengers]

Hi @hbucqp, there are \r (carriage return) characters in your fasta headers which might be introduced via a Windows-based text editor? If you remove those, Platon works as expected. There are 6 plasmid predicted contigs in your data. Please find a filtered fasta file below: test.fna.gz

Best regards!