<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>

CC BY-SA 3.0
2018-02-20T17:26:52.243Z
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'
Biomagician
CC BY-SA 3.0
2018-02-20T17:35:18.380Z
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.
heathobrien
CC BY-SA 3.0
2018-02-20T19:57:43.927Z
Do you use another tool to get EMBL files from GTF and FASTA?
Biomagician
CC BY-SA 3.0
2018-02-21T14:46:00.903Z
@charlesdarwin have you tried this to convert FASTA -> EMBL? http://sequenceconversion.bugaco.com/converter/biology/sequences/embl_to_fasta.php (no idea of how it works, but you can try)
aechchiki
CC BY-SA 3.0
2018-02-20T16:52:38.300Z
2018-02-20T16:52:38.300Z
heathobrien
<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>

CC BY-SA 3.0
2018-02-19T14:06:56.143Z
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)
llrs
CC BY-SA 3.0
2018-02-20T14:59:30.410Z
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.
Konrad Rudolph
<file-formats><format-conversion><gtf><emboss><seqret>
seqret: Warning: bad /protein_id value
# seqret: Warning: bad /protein_id value

(Asked by: username_0 on 2018-02-19)

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";

**Tags:** file-formats, format-conversion, gtf, emboss, seqret
> **Comments:**
> **username_1**: 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)  
> **username_2**: 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.  

---

## 1 answers

### Answer by username_3 on 2018-02-20. Score: 1

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/>

> **Comments:**
> **username_0**: 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'  
> **username_3**: 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.  
> **username_0**: Do you use another tool to get EMBL files from GTF and FASTA?  
> **username_4**: @charlesdarwin have you tried this to convert FASTA -> EMBL? http://sequenceconversion.bugaco.com/converter/biology/sequences/embl_to_fasta.php (no idea of how it works, but you can try)  

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