Answers.Body: <p>In short, the problem was solved by creating a temporary path file for igblast to look in because the <code>C:\Program Files</code> portion of the path has a space in it causing the error. Another potential solution is to install the igblast somewhere other than <code>C:\Program Files</code> .</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-08-16T13:55:38.600Z
Answers.LastActivityDate: 2024-08-16T13:55:38.600Z
Answers.UserDisplayName: majahi
Body: <p>I'm trying to run igblast from NCBI in windows powershell. When following the documentation and trying to run the following code:</p>
  <pre><code>bin/igblastn -germline_db_V database/mouse_gl_V -germline_db_J database/mouse_gl_J -germline_db_D database/mouse_gl_D -organism mouse -query myseq -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3
  </code></pre>
  <p>and</p>
  <pre><code>bin/igblastn -germline_db_V database/V.fasta -germline_db_J database/J.fasta -germline_db_D database/D.fasta -organism rhesus_monkey -query myseq -auxiliary_data optional_file/rhesus_monkey_gl.aux -show_translation 
  </code></pre>
  <p>I get the following errors:</p>
  <pre><code>BLAST query/options error: Germline annotation database C:\Program Files\NCBI\igblast-1.22.0\internal_data\mouse\mouse_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  </code></pre>
  <p>and</p>
  <pre><code>BLAST query/options error: Germline annotation database C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  </code></pre>
  <p>respectively.</p>
  <p>Additionally, I'm having issues running NCBI/igblast's and unable to create my own database references: <code>bin/edit_imgt_file.pl imgt_file &gt; my_seq_file</code> creates an empty <code>my_seq_file</code> and opens notepad with the code or prompt to choose a program to open the .pl</p>
  <p>I've tried using different os: Windows 10, 11, and on a virtual machine (Windows 11). On the virtual machine it doesn't return the error but it doesn't run either.</p>
  <p>Setting environment variables or designating a path hasn't helped.</p>
  <p>The following code:
  <code>dir C:\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*</code>
  yields:
  <code>dir : Cannot find path 'C:\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\' because it does not exist.</code>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-24T12:53:46.067Z
Comments.Text: Well, does the database exist? What is the output of `dir C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-24T14:13:30.277Z
Comments.Text: Hi, yes that database does exist. Within the `internal_data\rhesus_monkey` directory are 18 files `rhesus_monkey_V` with different file extensions such as `.ndb`, `.nhr`.
Comments.UserDisplayName: majahi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-24T14:25:39.837Z
Comments.Text: Please [edit] your question and show us the command you use to list the files and its output. And note that I didn't ask for `internal_data\rhesus_monkey`, I asked for `C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*`. That is important: the program isn't finding the files, and that is where it is looking. So either the files don't exist, or they exist but not where the program is trying to find them. And do you really get the same error with the two commands you show? They should be giving different errors since you gave different things to look for.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-24T14:41:31.533Z
Comments.Text: Yes I will edit that thank you. Yes that is correct, the error matches the last command but the first command produces the same error save for a different species, I will change the question to reflect that. `dir C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*` produces the following error: 
  `dir : Cannot find path 'C:\Program' because it does not exist.` 
  Thank you for your feedback
Comments.UserDisplayName: majahi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-24T15:07:17.220Z
Comments.Text: OK, so the issue is that you are running the commands from the wrong place. Please [edit] your question and add i) the full path (so `C:\whatever\whoever\something` and not just `whoever\something`) to the database files, ii) the full path of the directory you are launching the command from. I don't really know Windows so I can't help much with more specific commands, but presumably there is a way to find out your current dir in powershell.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-14T08:46:51.397Z
Comments.Text: In short, the problem was solved by creating a temporary path file for igblast to look in because the `C:\Program Files` portion of the path has a space in it causing the error. Another potential solution is to install the igblast somewhere other than `C:\Program Files` . Thank you for your help !
Comments.UserDisplayName: majahi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-14T10:17:34.467Z
Comments.Text: Can you please post that as an answer so the question can be marked as answered?
Comments.UserDisplayName: terdon
Tags: <blast><shell><windows>
Title: windows shell -- running igblast: "BLAST query/options error: Germline annotation database ... internal_data directory cannot be found"
ThreadText: # windows shell -- running igblast: "BLAST query/options error: Germline annotation database ... internal_data directory cannot be found"
  
  (Asked by: username_0 on 2024-07-24)
  
  I'm trying to run igblast from NCBI in windows powershell. When following the documentation and trying to run the following code:
  
  ```
  bin/igblastn -germline_db_V database/mouse_gl_V -germline_db_J database/mouse_gl_J -germline_db_D database/mouse_gl_D -organism mouse -query myseq -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3
  
  ```
  
  and
  
  ```
  bin/igblastn -germline_db_V database/V.fasta -germline_db_J database/J.fasta -germline_db_D database/D.fasta -organism rhesus_monkey -query myseq -auxiliary_data optional_file/rhesus_monkey_gl.aux -show_translation 
  
  ```
  
  I get the following errors:
  
  ```
  BLAST query/options error: Germline annotation database C:\Program Files\NCBI\igblast-1.22.0\internal_data\mouse\mouse_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  
  ```
  
  and
  
  ```
  BLAST query/options error: Germline annotation database C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V could not be found in [internal_data] directory
  Please refer to the BLAST+ user manual.
  
  ```
  
  respectively.
  
  Additionally, I'm having issues running NCBI/igblast's and unable to create my own database references: `bin/edit_imgt_file.pl imgt_file > my_seq_file` creates an empty `my_seq_file` and opens notepad with the code or prompt to choose a program to open the .pl
  
  I've tried using different os: Windows 10, 11, and on a virtual machine (Windows 11). On the virtual machine it doesn't return the error but it doesn't run either.
  
  Setting environment variables or designating a path hasn't helped.
  
  The following code:
  `dir C:\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*`
  yields:
  `dir : Cannot find path 'C:\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\' because it does not exist.`.
  
  **Tags:** blast, shell, windows
  
  > **Comments:**
  > **username_1**: Well, does the database exist? What is the output of `dir C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*`?  
  > **username_0**: Hi, yes that database does exist. Within the `internal_data\rhesus_monkey` directory are 18 files `rhesus_monkey_V` with different file extensions such as `.ndb`, `.nhr`.  
  > **username_1**: Please [edit] your question and show us the command you use to list the files and its output. And note that I didn't ask for `internal_data\rhesus_monkey`, I asked for `C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*`. That is important: the program isn't finding the files, and that is where it is looking. So either the files don't exist, or they exist but not where the program is trying to find them. And do you really get the same error with the two commands you show? They should be giving different errors since you gave different things to look for.  
  > **username_0**: Yes I will edit that thank you. Yes that is correct, the error matches the last command but the first command produces the same error save for a different species, I will change the question to reflect that. `dir C:\Program Files\NCBI\igblast-1.22.0\internal_data\rhesus_monkey\rhesus_monkey_V\*.*` produces the following error:  `dir : Cannot find path 'C:\Program' because it does not exist.`  Thank you for your feedback  
  > **username_1**: OK, so the issue is that you are running the commands from the wrong place. Please [edit] your question and add i) the full path (so `C:\whatever\whoever\something` and not just `whoever\something`) to the database files, ii) the full path of the directory you are launching the command from. I don't really know Windows so I can't help much with more specific commands, but presumably there is a way to find out your current dir in powershell.  
  > **username_0**: In short, the problem was solved by creating a temporary path file for igblast to look in because the `C:\Program Files` portion of the path has a space in it causing the error. Another potential solution is to install the igblast somewhere other than `C:\Program Files` . Thank you for your help !  
  > **username_1**: Can you please post that as an answer so the question can be marked as answered?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2024-08-16. Score: 1
  
  In short, the problem was solved by creating a temporary path file for igblast to look in because the `C:\Program Files` portion of the path has a space in it causing the error. Another potential solution is to install the igblast somewhere other than `C:\Program Files` .
  
  
  ---
  
  