Answers.Body: <p>@raysteven,</p>
  <p>If you follow the documnetation of BPGA at <a href="https://sourceforge.net/p/bpgatool/wiki/Home/" rel="nofollow noreferrer">https://sourceforge.net/p/bpgatool/wiki/Home/</a>, you can find the example of <strong>SUPPORTED INPUTS</strong> for all types of input files including gbk or gbff.
  Unfortunately, Prokka generated files are not supported due to different or missing tags than NCBI.</p>
  <p>One simple solution you may try is to edit your genBank file to include the tags such as <strong>/protein_id=&quot;Any_unique_protein_id_inside_quotes&quot;</strong> and everything else shown in the gbk example.</p>
  <p>I hope this helps.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-30T07:40:30.520Z
Answers.LastActivityDate: 2022-05-30T07:40:30.520Z
Answers.UserDisplayName: BioDeveloper
Body: <p>I'm trying to do pan-genome analysis using BPGA and I face this error:</p>
  <p><a href="https://i.sstatic.net/nyyXc.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/nyyXc.png" alt="enter image description here" /></a></p>
  <p><a href="https://i.sstatic.net/aIn26.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/aIn26.png" alt="enter image description here" /></a></p>
  <p><a href="https://i.sstatic.net/kijEl.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/kijEl.png" alt="enter image description here" /></a></p>
  <p>This error didn't show up in the other data set where all the .gbk is downloaded from NCBI. This .gbk file is our own data and has not been published in NCBI yet. There's of course protein data in it, there's this CDS qualifier &quot;translation&quot;, but somehow BPGA didn't detect this.</p>
  <p>The difference between our data and NCBI data is that most of the NCBI .gbk files are annotated with PGAP. On the other hand, our .gbk is annotated with Prokka (have tried it in DFAST and KBase). NCBI .gbk files that are annotated with PGAP have this CDS qualifier &quot;protein_id&quot; in them. Besides that, I don't think there's any difference.</p>
  <p>Does the BPGA script counts the protein number based on the &quot;protein_id&quot; qualifier? How should I solve this? I can't annotate the .fasta file with PGAP because it's so resource-intensive. I believe that, if Prokka is installed locally, there's this <a href="https://github.com/tseemann/prokka/issues/121#issuecomment-113965257" rel="nofollow noreferrer">&quot;--compliant&quot;</a> option that can integrate the &quot;protein_id&quot; qualifier into the output .gbk file. I have tried to install Prokka locally, but it didn't run well too, I encountered another <a href="https://github.com/bioconda/bioconda-recipes/issues/10277" rel="nofollow noreferrer">error</a> for that and all the solutions didn't work for me.</p>
  <p>Any opinion on this issue? Thanks for reading my question.</p>
  <p>EDIT:
  I tried to insert one dummy &quot;protein_id&quot; on my Prokka-annotated .gbk files and it run perfectly without errors.</p>
  <p><a href="https://i.sstatic.net/wR2XP.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/wR2XP.png" alt="enter image description here" /></a></p>
  <p>But when I tried to insert dummy protein_id on my DFAST-annotated .gbk files, it won't run and faced another error. What is this &quot;protein_id&quot; really defined by the script?</p>
  
Tags: <perl><sequence-annotation>
Title: BPGA error: there was no protein data in file
ThreadText: # BPGA error: there was no protein data in file
  
  (Asked by: username_0 on 2022-03-13)
  
  I'm trying to do pan-genome analysis using BPGA and I face this error:
  
  [![enter image description here](https://i.sstatic.net/nyyXc.png)](https://i.sstatic.net/nyyXc.png)
  
  [![enter image description here](https://i.sstatic.net/aIn26.png)](https://i.sstatic.net/aIn26.png)
  
  [![enter image description here](https://i.sstatic.net/kijEl.png)](https://i.sstatic.net/kijEl.png)
  
  This error didn't show up in the other data set where all the .gbk is downloaded from NCBI. This .gbk file is our own data and has not been published in NCBI yet. There's of course protein data in it, there's this CDS qualifier "translation", but somehow BPGA didn't detect this.
  
  The difference between our data and NCBI data is that most of the NCBI .gbk files are annotated with PGAP. On the other hand, our .gbk is annotated with Prokka (have tried it in DFAST and KBase). NCBI .gbk files that are annotated with PGAP have this CDS qualifier "protein\_id" in them. Besides that, I don't think there's any difference.
  
  Does the BPGA script counts the protein number based on the "protein\_id" qualifier? How should I solve this? I can't annotate the .fasta file with PGAP because it's so resource-intensive. I believe that, if Prokka is installed locally, there's this ["--compliant"](https://github.com/tseemann/prokka/issues/121#issuecomment-113965257) option that can integrate the "protein\_id" qualifier into the output .gbk file. I have tried to install Prokka locally, but it didn't run well too, I encountered another [error](https://github.com/bioconda/bioconda-recipes/issues/10277) for that and all the solutions didn't work for me.
  
  Any opinion on this issue? Thanks for reading my question.
  
  EDIT:
  I tried to insert one dummy "protein\_id" on my Prokka-annotated .gbk files and it run perfectly without errors.
  
  [![enter image description here](https://i.sstatic.net/wR2XP.png)](https://i.sstatic.net/wR2XP.png)
  
  But when I tried to insert dummy protein\_id on my DFAST-annotated .gbk files, it won't run and faced another error. What is this "protein\_id" really defined by the script?
  
  **Tags:** perl, sequence-annotation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-05-30. Score: 1
  
  @username_0,
  
  If you follow the documnetation of BPGA at <https://sourceforge.net/p/bpgatool/wiki/Home/>, you can find the example of **SUPPORTED INPUTS** for all types of input files including gbk or gbff.
  Unfortunately, Prokka generated files are not supported due to different or missing tags than NCBI.
  
  One simple solution you may try is to edit your genBank file to include the tags such as **/protein\_id="Any\_unique\_protein\_id\_inside\_quotes"** and everything else shown in the gbk example.
  
  I hope this helps.
  
  
  ---
  
  