Body: <p>As you know, ncbi has several databases, including nt, nr, etc.
  What I am going to do is to blast a sequence of approximately 30 base pairs to the nr database and extract all similar sequences.
  For this purpose, with the help of YouTube, I downloaded and installed Command Line Blast on my Windows PC.</p>
  <p>Then, from the database section I downloaded all the nr databases, which were 83 zip files and 200 GB in size.  Then, I unzipped it and stored it to a folder on my computer.</p>
  <p>Because I saw that the size of the first two zip files that came out of the zip increased from 25 GB to 50 GB, I only unzipped two files to see if my command line works or not.</p>
  <p>So my database became a folder of almost 50 GB.</p>
  <p>Then I ran the simplest command in the cmd of my computer.</p>
  <pre><code>blastn -query D:\query.fa -out D:\results.txt -db D:\nrDataBase
  </code></pre>
  <p>It's been almost two weeks now that I'm stuck day and night with this simple line of code and it doesn't work.</p>
  <p>It says once that the query file is not accessible. Once it says that no suitable files were found in the database, etc.</p>
  <p>I tested every solution that came to my mind, I used the text format for the query, but it didn't work</p>
  <p>I downloaded one or two files from the nt database, I said maybe there is a problem with the nr database, but it still didn't work.
  I made a small fasta file, introduced it as a database, but it still didn't accept.</p>
  <p>I tried also on the Macbook, it still didn't work, either the query got an error or the database.</p>
  <p>The blast has been well installed, When using -h it shows the full info of the tool. It doesn’t work means that I encounter different errors like: The query is not acceptable Or The alias or index file is found in the database I encounter these errors while e. g., the query file is a normal fasta file. I mean, the errors don’t seem to be logical, it looks like something else is going wrong.</p>
  <p>I'm really upset, I told you to send me a message to see if you can help me.</p>
  <p>Thank you very much and sorry for the long message.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-02T13:42:39.400Z
Comments.Text: "it doesn't work" is not enough information. What do you see on the command prompt when you just run `blastn -h`?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-02T15:08:19.843Z
Comments.Text: @M__ the question was migrated; the OP does not have a profile on bioinfo SE yet.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-02T15:51:07.037Z
Comments.Text: Thanks @RamRS of course I should have spotted.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-02T19:38:55.020Z
Comments.Text: You state that you are not using the entire database, you're using just a subset of the resource files. That could be causing the error. Just because you're using a subset of the resource files does not mean you're picking a functional subset of the database.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-04T02:53:39.063Z
Comments.Text: Please provide more context around what you want to do. It is not necessary to download the entirety of the *nr* database in order to extract only the sequences that match a specific subsequence. There's probably a better way to achieve your goal without massive downloads.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-04T03:13:01.777Z
Comments.Text: try running `makeblastdb` on your downloaded database files, then re-run your blast command
Comments.UserDisplayName: user3479780
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-13T20:28:38.113Z
Comments.Text: Are you working in the correct directory? Meaning, are you in the directory of the script you are trying to run? What did the error message look like? Please run again and provide that detail so it gives us more to work with!:)
Comments.UserDisplayName: Rachel Sweeney
Tags: <blast>
Title: BLAST+ not working on my Command Line
ThreadText: # BLAST+ not working on my Command Line
  
  (Asked by: username_0 on 2023-10-02)
  
  As you know, ncbi has several databases, including nt, nr, etc.
  What I am going to do is to blast a sequence of approximately 30 base pairs to the nr database and extract all similar sequences.
  For this purpose, with the help of YouTube, I downloaded and installed Command Line Blast on my Windows PC.
  
  Then, from the database section I downloaded all the nr databases, which were 83 zip files and 200 GB in size. Then, I unzipped it and stored it to a folder on my computer.
  
  Because I saw that the size of the first two zip files that came out of the zip increased from 25 GB to 50 GB, I only unzipped two files to see if my command line works or not.
  
  So my database became a folder of almost 50 GB.
  
  Then I ran the simplest command in the cmd of my computer.
  
  ```
  blastn -query D:\query.fa -out D:\results.txt -db D:\nrDataBase
  
  ```
  
  It's been almost two weeks now that I'm stuck day and night with this simple line of code and it doesn't work.
  
  It says once that the query file is not accessible. Once it says that no suitable files were found in the database, etc.
  
  I tested every solution that came to my mind, I used the text format for the query, but it didn't work
  
  I downloaded one or two files from the nt database, I said maybe there is a problem with the nr database, but it still didn't work.
  I made a small fasta file, introduced it as a database, but it still didn't accept.
  
  I tried also on the Macbook, it still didn't work, either the query got an error or the database.
  
  The blast has been well installed, When using -h it shows the full info of the tool. It doesn’t work means that I encounter different errors like: The query is not acceptable Or The alias or index file is found in the database I encounter these errors while e. g., the query file is a normal fasta file. I mean, the errors don’t seem to be logical, it looks like something else is going wrong.
  
  I'm really upset, I told you to send me a message to see if you can help me.
  
  Thank you very much and sorry for the long message.
  
  **Tags:** blast
  
  > **Comments:**
  > **username_1**: "it doesn't work" is not enough information. What do you see on the command prompt when you just run `blastn -h`?  
  > **username_1**: @username_2 the question was migrated; the OP does not have a profile on bioinfo SE yet.  
  > **username_2**: Thanks @username_1 of course I should have spotted.  
  > **username_1**: You state that you are not using the entire database, you're using just a subset of the resource files. That could be causing the error. Just because you're using a subset of the resource files does not mean you're picking a functional subset of the database.  
  > **username_3**: Please provide more context around what you want to do. It is not necessary to download the entirety of the *nr* database in order to extract only the sequences that match a specific subsequence. There's probably a better way to achieve your goal without massive downloads.  
  > **username_4**: try running `makeblastdb` on your downloaded database files, then re-run your blast command  
  > **username_5**: Are you working in the correct directory? Meaning, are you in the directory of the script you are trying to run? What did the error message look like? Please run again and provide that detail so it gives us more to work with!:)  
  
  ---
  
  ## 0 answers
  
  