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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";
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    $\begingroup$ To me it looks like a bug, where the encoding or the quotes are not properly handled. (ie, CCE57754 would be a valid protien_id(?) but "CCE57754" it isn't) $\endgroup$
    – llrs
    Feb 19, 2018 at 14:06
  • $\begingroup$ Can you show (a small part of) your GTF file? I tend to agree with Llopis, but not all fields in the GTF files can be quoted. $\endgroup$
    – Konrad Rudolph
    Feb 20, 2018 at 14:59

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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/

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  • $\begingroup$ I tried with gff2 but I get the same problem: Warning: bad /protein_id value 'CCQ26880' Warning: bad /protein_id value 'CCQ26881' Warning: bad /protein_id value 'CCQ26882' Warning: bad /protein_id value 'CCQ26883' $\endgroup$
    – Biomagician
    Feb 20, 2018 at 17:26
  • $\begingroup$ If your copying the output directly, that's a different problem ('CCQ26880' vs. '''CCQ26880"'). It looks like it's parsing the GTF correctly but choking on the values for some reason. I'm not very familiar with this tool so I can't advise further. $\endgroup$
    – heathobrien
    Feb 20, 2018 at 17:35
  • $\begingroup$ Do you use another tool to get EMBL files from GTF and FASTA? $\endgroup$
    – Biomagician
    Feb 20, 2018 at 19:57
  • $\begingroup$ @charlesdarwin have you tried this to convert FASTA -> EMBL? sequenceconversion.bugaco.com/converter/biology/sequences/… (no idea of how it works, but you can try) $\endgroup$
    – aechchiki
    Feb 21, 2018 at 14:46

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