Body: <p>I'm in the following situation and I came here to see if I could get some help.</p>
  <p>I'd like to use IgBLAST for an analysis on some Alpaca antibody data, so I received some FASTA sequences from a colleague, <code>imgt_gapped_alpaca_IGHV.fasta</code>, <code>imgt_gapped_alpaca_IGHD.fasta</code>, etc.</p>
  <p>I used the <code>edit_imgt_file.pl</code> tool to appropriately structure each <code>.fasta</code> file, and to make a BLAST database for each (V, D, J) segment:</p>
  <pre><code># Process V segment sequences with edit_imgt_file
  edit_imgt_file.pl \
  ~/VHH/data/imgt-data/imgt_gapped_alpaca_IGHV.fasta &gt; ~/ncbi-igblast-1.21.0/internal_data/alpaca/imgt_alpaca_ig_v.fasta
  
  makeblastdb -parse_seqids -dbtype nucl \
      -in ~/ncbi-igblast-1.21.0/internal_data/alpaca/imgt_alpaca_ig_v.fasta \
      -out ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_V
  </code></pre>
  <p>After doing that for each of the segments, I went to put all the pieces together and perform the following query:</p>
  <pre><code>igblastn \
      -germline_db_V ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_V \
      -germline_db_D ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_D \
      -germline_db_J ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_J \
      -auxiliary_data ~/ncbi-igblast-1.21.0/optional_file/alpaca_gl.aux \
      -domain_system imgt -ig_seqtype Ig -organism alpaca \
      -outfmt '7 std qseq sseq btop' \
      -query ~/VHH/data/ALPACA1-BC1.fastq \
      -out ~/VHH/data/igblast-out/ALPACA1-BC1.fmt7
  </code></pre>
  <p>Unfortunately, the following error is returned to me:</p>
  <pre><code>BLAST query/options error: Germline annotation database alpaca/alpaca_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  </code></pre>
  <p>I've searched the internet high and low, but this appears to be a bit of a niche problem, and the BLAST+ user manual promised a little more than it was able to deliver in terms of helpful suggestions.</p>
  <p>Any questions/comments/ideas/diagnostics would be very welcome-- if you see any low hanging fruit, please let me know-- thank you so much for your time!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-17T15:31:36.320Z
Comments.Text: What you have looks like the right idea to me.  (I use igblastn regularly for human and rhesus macaque antibodies with custom DB+aux files, but not with a custom organism label itself.)  What files do you see in your alpaca db dir for V/D/J?  Are both igblastn and makeblastdb definitely coming from igblast 1.21.0?  (Any chance something's mismatched between those two binaries, I wonder?)  And where did your alpaca auxiliary file come from?  You could maybe drop the aux part to simplify things while troubleshooting.
Comments.UserDisplayName: Jesse
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-17T15:38:43.787Z
Comments.Text: Actually I get the same error if I just change my human or rhesus commands to some arbitrary organism name.  Did you also create the FWR/CDR file like it talks about [here](https://ncbi.github.io/igblast/cook/How-to-set-up.html#procedure-to-set-up-igblast-for-custom-organism)?  I guess all of my questions really boil down to, what's in your `~/ncbi-igblast-1.21.0/internal_data/alpaca` directory?
Comments.UserDisplayName: Jesse
Tags: <blast><blastn><makeblastdb>
Title: IgBLAST Error: Germline annotation database could not be found in [internal_data] directory
ThreadText: # IgBLAST Error: Germline annotation database could not be found in [internal_data] directory
  
  (Asked by: username_0 on 2023-08-16)
  
  I'm in the following situation and I came here to see if I could get some help.
  
  I'd like to use IgBLAST for an analysis on some Alpaca antibody data, so I received some FASTA sequences from a colleague, `imgt_gapped_alpaca_IGHV.fasta`, `imgt_gapped_alpaca_IGHD.fasta`, etc.
  
  I used the `edit_imgt_file.pl` tool to appropriately structure each `.fasta` file, and to make a BLAST database for each (V, D, J) segment:
  
  ```
  # Process V segment sequences with edit_imgt_file
  edit_imgt_file.pl \
  ~/VHH/data/imgt-data/imgt_gapped_alpaca_IGHV.fasta > ~/ncbi-igblast-1.21.0/internal_data/alpaca/imgt_alpaca_ig_v.fasta
  
  makeblastdb -parse_seqids -dbtype nucl \
      -in ~/ncbi-igblast-1.21.0/internal_data/alpaca/imgt_alpaca_ig_v.fasta \
      -out ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_V
  
  ```
  
  After doing that for each of the segments, I went to put all the pieces together and perform the following query:
  
  ```
  igblastn \
      -germline_db_V ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_V \
      -germline_db_D ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_D \
      -germline_db_J ~/ncbi-igblast-1.21.0/internal_data/alpaca/alpaca_J \
      -auxiliary_data ~/ncbi-igblast-1.21.0/optional_file/alpaca_gl.aux \
      -domain_system imgt -ig_seqtype Ig -organism alpaca \
      -outfmt '7 std qseq sseq btop' \
      -query ~/VHH/data/ALPACA1-BC1.fastq \
      -out ~/VHH/data/igblast-out/ALPACA1-BC1.fmt7
  
  ```
  
  Unfortunately, the following error is returned to me:
  
  ```
  BLAST query/options error: Germline annotation database alpaca/alpaca_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  
  ```
  
  I've searched the internet high and low, but this appears to be a bit of a niche problem, and the BLAST+ user manual promised a little more than it was able to deliver in terms of helpful suggestions.
  
  Any questions/comments/ideas/diagnostics would be very welcome-- if you see any low hanging fruit, please let me know-- thank you so much for your time!
  
  **Tags:** blast, blastn, makeblastdb
  
  > **Comments:**
  > **username_1**: What you have looks like the right idea to me.  (I use igblastn regularly for human and rhesus macaque antibodies with custom DB+aux files, but not with a custom organism label itself.)  What files do you see in your alpaca db dir for V/D/J?  Are both igblastn and makeblastdb definitely coming from igblast 1.21.0?  (Any chance something's mismatched between those two binaries, I wonder?)  And where did your alpaca auxiliary file come from?  You could maybe drop the aux part to simplify things while troubleshooting.  
  > **username_1**: Actually I get the same error if I just change my human or rhesus commands to some arbitrary organism name.  Did you also create the FWR/CDR file like it talks about [here](https://ncbi.github.io/igblast/cook/How-to-set-up.html#procedure-to-set-up-igblast-for-custom-organism)?  I guess all of my questions really boil down to, what's in your `~/ncbi-igblast-1.21.0/internal_data/alpaca` directory?  
  
  ---
  
  ## 0 answers
  
  