text: user1075: I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence:
  seqret -sequence ecoli.fa -feature -fformat gff -fopenfile ecoli.gtf -osformat embl -auto -outseq ecoli.embl
  
  It produces my desired EMBL file but it warns against a 'bad protein_id':
  ...
  Warning: bad /protein_id value '"CCE57732"'
  Warning: bad /protein_id value '"CCE57733"'
  Warning: bad /protein_id value '"CCE57734"'
  Warning: bad /protein_id value '"CCE57735"'
  Warning: bad /protein_id value '"CCE57754"'
  
  What's wrong with these protein IDs? The organism I am working with is Escherichia coli.
  Here are a few lines from my GTF file. The first line has a protein_id.
  Chromosome      ena     CDS     349     2808    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding"; protein_id "CCQ26880";
  Chromosome      ena     start_codon     349     351     .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  Chromosome      ena     stop_codon      2809    2811    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  
  
  user581: You're supplying a GTF feature file, but telling it that the features are in GFF3 format. I think you need -fformat gff2. See https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/
  
original_text: 1075: <p>I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence:</p>
  
  <pre><code>seqret -sequence ecoli.fa -feature -fformat gff -fopenfile ecoli.gtf -osformat embl -auto -outseq ecoli.embl
  </code></pre>
  
  <p>It produces my desired EMBL file but it warns against a 'bad protein_id':</p>
  
  <pre><code>...
  Warning: bad /protein_id value '"CCE57732"'
  Warning: bad /protein_id value '"CCE57733"'
  Warning: bad /protein_id value '"CCE57734"'
  Warning: bad /protein_id value '"CCE57735"'
  Warning: bad /protein_id value '"CCE57754"'
  </code></pre>
  
  <p>What's wrong with these protein IDs? The organism I am working with is <em>Escherichia coli</em>.</p>
  
  <p>Here are a few lines from my GTF file. The first line has a protein_id.</p>
  
  <pre><code>Chromosome      ena     CDS     349     2808    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding"; protein_id "CCQ26880";
  Chromosome      ena     start_codon     349     351     .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  Chromosome      ena     stop_codon      2809    2811    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  </code></pre>
   581: <p>You're supplying a GTF feature file, but telling it that the features are in GFF3 format. I think you need <code>-fformat gff2</code>. See <a href="https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/" rel="nofollow noreferrer">https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/</a></p>
  